Index (baseCode 0.2.5 API)

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A

AFFX - Static variable in class baseCode.dataFilter.AffymetrixProbeNameFilter: Filter probes that have the AFFX prefix.
AFFX - Static variable in class baseCode.dataFilter.RowAffyNameFilter: Filter probes that have the AFFX prefix.
ASCENDING - Static variable in class baseCode.gui.table.TableSorter
AbstractFilter - class baseCode.dataFilter.AbstractFilter.: Base implementation of the filter class.
AbstractFilter() - Constructor for class baseCode.dataFilter.AbstractFilter
AbstractGraph - class baseCode.dataStructure.graph.AbstractGraph.: Copyright (c) Columbia University
AbstractGraph() - Constructor for class baseCode.dataStructure.graph.AbstractGraph
AbstractGraph(Set) - Constructor for class baseCode.dataStructure.graph.AbstractGraph: Create a new graph from a set of nodes.
AbstractGraphNode - class baseCode.dataStructure.graph.AbstractGraphNode.: Copyright (c) Columbia University
AbstractGraphNode(Object, Object, Graph) - Constructor for class baseCode.dataStructure.graph.AbstractGraphNode: Create a new node with key and value given.
AbstractGraphNode(Object) - Constructor for class baseCode.dataStructure.graph.AbstractGraphNode: Create a new node when given only a key.
AbstractLevelFilter - class baseCode.dataFilter.AbstractLevelFilter.: Abstract class representing a filter that removes things from matrices based on the values themselves.
AbstractLevelFilter() - Constructor for class baseCode.dataFilter.AbstractLevelFilter
AbstractNamedDoubleMatrix - class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix.
AbstractNamedDoubleMatrix() - Constructor for class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix
AbstractNamedMatrix - class baseCode.dataStructure.matrix.AbstractNamedMatrix.: Copyright (c) 2004 Columbia University
AbstractNamedMatrix() - Constructor for class baseCode.dataStructure.matrix.AbstractNamedMatrix
AbstractNamedMatrixReader - class baseCode.io.reader.AbstractNamedMatrixReader.: Abstract class representing an object that can read in a NamedMatrixfrom a file.
AbstractNamedMatrixReader() - Constructor for class baseCode.io.reader.AbstractNamedMatrixReader
AffymetrixProbeNameFilter - class baseCode.dataFilter.AffymetrixProbeNameFilter.: Remove probes that have names meeting certain rules indicating they may have low reliability.
AffymetrixProbeNameFilter(int[]) - Constructor for class baseCode.dataFilter.AffymetrixProbeNameFilter
AffymetrixProbeNameFilter() - Constructor for class baseCode.dataFilter.AffymetrixProbeNameFilter: Filter probes with all criteria switched on.
Algorithm - class baseCode.algorithm.Algorithm.
Algorithm() - Constructor for class baseCode.algorithm.Algorithm
AppDialog - class baseCode.gui.AppDialog.: Title:
AppDialog() - Constructor for class baseCode.gui.AppDialog
AppDialog(JFrame, int, int) - Constructor for class baseCode.gui.AppDialog
AverageLinkageDistancer - class baseCode.algorithm.learning.unsupervised.cluster.AverageLinkageDistancer.
AverageLinkageDistancer() - Constructor for class baseCode.algorithm.learning.unsupervised.cluster.AverageLinkageDistancer
accept(File) - Method in class baseCode.gui.file.DataFileFilter
accept(File) - Method in class baseCode.gui.file.ImageFileFilter
accept(File) - Method in class baseCode.gui.file.XMLFileFilter
actionButton - Variable in class baseCode.gui.AppDialog
actionButton_actionPerformed(ActionEvent) - Method in class baseCode.gui.AppDialog
actionPerformed(ActionEvent) - Method in class baseCode.gui.JWebBrowser
addChild(Object) - Method in class baseCode.dataStructure.graph.DirectedGraphNode
addChildTo(Object, Object, Object) - Method in class baseCode.dataStructure.graph.DirectedGraph: Add a child to a particualar node identified by key.
addChildTo(Object, Object) - Method in class baseCode.dataStructure.graph.DirectedGraph: Add a child to a particular node identified by key; if the node is not in the graph, an exception is thrown.
addClass(String, String) - Method in class baseCode.bio.geneset.GONames
addClass(String, ArrayList) - Method in class baseCode.bio.geneset.GeneAnnotations: Add a class
addColumnName(String) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix: Add a column name when we don't care what the index will be.
addColumnName(String, int) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
addColumnName(String, int) - Method in interface baseCode.dataStructure.matrix.NamedMatrix: Add a column name associated with an index.
addDataExtension(String) - Static method in class baseCode.util.FileTools
addHelp(String) - Method in class baseCode.gui.AppDialog
addHelp(String) - Method in class baseCode.gui.WizardStep
addImageExtension(String) - Static method in class baseCode.util.FileTools
addItem(Cluster) - Method in class baseCode.algorithm.learning.unsupervised.cluster.Cluster
addMain(JPanel) - Method in class baseCode.gui.AppDialog
addMain(JPanel) - Method in class baseCode.gui.WizardStep
addNode(GraphNode) - Method in class baseCode.dataStructure.graph.AbstractGraph
addNode(Object, Object) - Method in class baseCode.dataStructure.graph.DirectedGraph
addNode(Object, Object) - Method in interface baseCode.dataStructure.graph.Graph
addParent(Object) - Method in class baseCode.dataStructure.graph.DirectedGraphNode
addParentTo(Object, Object, Object) - Method in class baseCode.dataStructure.graph.DirectedGraph
addParentTo(Object, Object) - Method in class baseCode.dataStructure.graph.DirectedGraph
addRow(String, IntArrayList, DoubleArrayList) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
addRow(String, DoubleMatrix1D) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
addRowName(String) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix: Add a row name when we don't care what the index will be.
addRowName(String, int) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix
addRowName(String, int) - Method in interface baseCode.dataStructure.matrix.NamedMatrix: Add a row name associated with a row index.
addStep(int, WizardStep) - Method in class baseCode.gui.Wizard
aroc(int, Set) - Static method in class baseCode.math.ROC: Calculate area under ROC.
aroc(int, Set, int) - Static method in class baseCode.math.ROC: Calculate area under ROC, up to a given number of False positives.
assign(DoubleFunction) - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D: WARNING this only even assigns to the non-empty values, for performance reasons.
autoCorrelation(DoubleArrayList, int, double, double) - Static method in class baseCode.math.DescriptiveWithMissing: Not supported.

B

BLACKBODY_COLORMAP - Static variable in class baseCode.gui.ColorMap

BenjaminiHochbergCut(DoubleArrayList, double) - Static method in class baseCode.math.MultipleTestCorrection
Benjamini-Hochberg method.
BinaryTree - class baseCode.dataStructure.tree.BinaryTree.

BinaryTree(BinaryTreeNode) - Constructor for class baseCode.dataStructure.tree.BinaryTree

BinaryTree() - Constructor for class baseCode.dataStructure.tree.BinaryTree

BinaryTreeNode - class baseCode.dataStructure.tree.BinaryTreeNode.

BinaryTreeNode(Object) - Constructor for class baseCode.dataStructure.tree.BinaryTreeNode

BinaryTreeNode() - Constructor for class baseCode.dataStructure.tree.BinaryTreeNode

BonferroniCut(DoubleArrayList, double) - Static method in class baseCode.math.MultipleTestCorrection
Determine the Bonferroni pvalue threshold to maintain the family wise error rate (assuming pvalues are independent).
BottomPanel - Variable in class baseCode.gui.Wizard

BottomPanelWrap - Variable in class baseCode.gui.Wizard

BrowserLauncher - class baseCode.util.BrowserLauncher.
BrowserLauncher is a class that provides one static method, openURL, which opens the default web browser for the current user of the system to the given URL.
ByteArrayConverter - class baseCode.io.ByteArrayConverter.
Class to convert byte arrays (e.g., Blobs) to and from other types of arrays.
ByteArrayConverter() - Constructor for class baseCode.io.ByteArrayConverter

backButton - Variable in class baseCode.gui.Wizard

backButton_actionPerformed(ActionEvent) - Method in class baseCode.gui.Wizard
Define what happens when the 'back' button is pressed
baseCode.algorithm - package baseCode.algorithm

baseCode.algorithm.learning.unsupervised - package baseCode.algorithm.learning.unsupervised

baseCode.algorithm.learning.unsupervised.cluster - package baseCode.algorithm.learning.unsupervised.cluster

baseCode.bio - package baseCode.bio

baseCode.bio.geneset - package baseCode.bio.geneset

baseCode.common - package baseCode.common

baseCode.dataFilter - package baseCode.dataFilter

baseCode.dataStructure - package baseCode.dataStructure

baseCode.dataStructure.graph - package baseCode.dataStructure.graph

baseCode.dataStructure.matrix - package baseCode.dataStructure.matrix

baseCode.dataStructure.tree - package baseCode.dataStructure.tree

baseCode.db - package baseCode.db

baseCode.graphics.text - package baseCode.graphics.text

baseCode.gui - package baseCode.gui

baseCode.gui.file - package baseCode.gui.file

baseCode.gui.table - package baseCode.gui.table

baseCode.io - package baseCode.io

baseCode.io.reader - package baseCode.io.reader

baseCode.io.writer - package baseCode.io.writer

baseCode.math - package baseCode.math

baseCode.math.distribution - package baseCode.math.distribution

baseCode.math.metaanalysis - package baseCode.math.metaanalysis

baseCode.misc - package baseCode.misc

baseCode.util - package baseCode.util

baseCode.xml - package baseCode.xml

best() - Method in class baseCode.algorithm.Ranker

byteArrayToAsciiString(byte[]) - Method in class baseCode.io.ByteArrayConverter
Convert a byte array with one-byte-per-character ASCII encoding (aka ISO-8859-1).
byteArrayToChars(byte[]) - Method in class baseCode.io.ByteArrayConverter

byteArrayToDoubles(byte[]) - Method in class baseCode.io.ByteArrayConverter

byteArrayToInts(byte[]) - Method in class baseCode.io.ByteArrayConverter

byteArrayToLongs(byte[]) - Method in class baseCode.io.ByteArrayConverter

byteToCorrel(int) - Static method in class baseCode.math.CorrelationStats

byteToPvalue(int) - Static method in class baseCode.math.CorrelationStats

C

COLORS - Static variable in class baseCode.gui.table.JBarGraphCellRenderer

COMPARABLE_COMAPRATOR - Static variable in class baseCode.gui.table.TableSorter

CV - Static variable in class baseCode.dataFilter.RowLevelFilter
Use the coefficient of variation as the criterion
Cluster - class baseCode.algorithm.learning.unsupervised.cluster.Cluster.

Cluster() - Constructor for class baseCode.algorithm.learning.unsupervised.cluster.Cluster

Cluster(Object, Distancer) - Constructor for class baseCode.algorithm.learning.unsupervised.cluster.Cluster

Cluster(Collection, Distancer) - Constructor for class baseCode.algorithm.learning.unsupervised.cluster.Cluster

ClusteringAlgorithm - class baseCode.algorithm.learning.unsupervised.cluster.ClusteringAlgorithm.

ClusteringAlgorithm() - Constructor for class baseCode.algorithm.learning.unsupervised.cluster.ClusteringAlgorithm

ColorMap - class baseCode.gui.ColorMap.
Title: ColorMap
ColorMap() - Constructor for class baseCode.gui.ColorMap

ColorMap(int) - Constructor for class baseCode.gui.ColorMap

ColorMap(Color[]) - Constructor for class baseCode.gui.ColorMap

ColorMap(int, Color[]) - Constructor for class baseCode.gui.ColorMap
Pre-condition: suggestedNumberOfColors > colorMap.length
ColorMatrix - class baseCode.gui.ColorMatrix.
Title: ColorMatrix
ColorMatrix(String) - Constructor for class baseCode.gui.ColorMatrix

ColorMatrix(DenseDoubleMatrix2DNamed) - Constructor for class baseCode.gui.ColorMatrix

ColorMatrix(String, Color[], Color) - Constructor for class baseCode.gui.ColorMatrix

ColorMatrix(AbstractNamedDoubleMatrix, Color[], Color) - Constructor for class baseCode.gui.ColorMatrix

Constants - class baseCode.math.Constants.
Used in some ports of statistical code.
Constants() - Constructor for class baseCode.math.Constants

CorrelationEffectMetaAnalysis - class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis.
Implementation of meta-analysis of correlations along the lines of chapter 18 of Cooper and Hedges, "Handbook of Research Synthesis".
CorrelationEffectMetaAnalysis(boolean, boolean) - Constructor for class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis

CorrelationEffectMetaAnalysis() - Constructor for class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis

CorrelationStats - class baseCode.math.CorrelationStats.
Statistical evaluation and transformation tools for correlations.
CorrelationStats() - Constructor for class baseCode.math.CorrelationStats

callingframe - Variable in class baseCode.gui.AppDialog

callingframe - Variable in class baseCode.gui.Wizard

cancelButton - Variable in class baseCode.gui.AppDialog

cancelButton - Variable in class baseCode.gui.Wizard

cancelButton_actionPerformed(ActionEvent) - Method in class baseCode.gui.AppDialog

cancelButton_actionPerformed(ActionEvent) - Method in class baseCode.gui.Wizard
Define what happens when the 'cancel' button is pressed.
cancelSorting() - Method in class baseCode.gui.table.TableSorter

cardinality() - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed

cdf(DoubleArrayList) - Static method in class baseCode.math.Stats
Convert an array into a cumulative density function (CDF).
changeExtension(String, String) - Static method in class baseCode.util.FileTools

charArrayToBytes(char[]) - Method in class baseCode.io.ByteArrayConverter

checkPathIsReadableFile(String) - Static method in class baseCode.util.FileTools

children - Variable in class baseCode.dataStructure.graph.DirectedGraphNode

chooserandom(double[], double[], int[], int, int) - Static method in class baseCode.math.RandomChooser
Fill randomvals with random things from sourcedata, without replacement.
chooserandom(int[], int[], int, int) - Static method in class baseCode.math.RandomChooser
choose n random integers from 0 to max without repeating
chooserandom(int[], boolean[], int, int) - Static method in class baseCode.math.RandomChooser
choose n random integers from 0 to max without repeating
chooserandomWrep(int[], int, int) - Static method in class baseCode.math.RandomChooser
Same as chooserandom, but with replacement -- that is, repeats are allowed.
clear() - Method in class baseCode.gui.StatusJlabel

clear() - Method in class baseCode.util.StatusDebugLogger

clear() - Method in class baseCode.util.StatusStderr

clear() - Method in interface baseCode.util.StatusViewer
Clear the status dislay.
clearStatus() - Method in class baseCode.gui.Wizard
Make the status bar empty.
clone() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
Makes a copy of this node.
clone() - Method in class baseCode.gui.ColorMatrix

closeCon() - Method in class baseCode.db.Handle
Close the database connection.
closeEnough(DoubleArrayList, DoubleArrayList, double) - Static method in class baseCode.util.RegressionTesting
Test whether two DoubleArrayLists are 'close enough' to call equal.
closeEnough(AbstractNamedDoubleMatrix, AbstractNamedDoubleMatrix, double) - Static method in class baseCode.util.RegressionTesting
Test whether two AbstractNamedDoubleMatrix are 'close enough' to call equal.
closeEnough(DoubleMatrix2D, DoubleMatrix2D, double) - Static method in class baseCode.util.RegressionTesting

closeEnough(Object[], Object[]) - Static method in class baseCode.util.RegressionTesting
Test whether two object arrays are the same.
collapseGeneSets(GeneAnnotations, StatusViewer) - Static method in class baseCode.bio.geneset.GeneSetMapTools
Identify classes which are absoluely identical to others.
columns() - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix

columns() - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

columns() - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed

columns() - Method in interface baseCode.dataStructure.matrix.NamedMatrix
Get the number of columns the matrix has.
columns() - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed

columns() - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed

columns() - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed

compare(double, int, double, int) - Static method in class baseCode.math.CorrelationStats
Statistical comparison of two correlations.
compareTo(Object) - Method in class baseCode.algorithm.learning.unsupervised.cluster.Cluster

compareTo(Object) - Method in class baseCode.dataStructure.graph.DirectedGraphNode
Uses the topological sort order.
compareTo(Object) - Method in class baseCode.dataStructure.graph.UndirectedGraphNode

compareTo(Object) - Method in class baseCode.dataStructure.tree.BinaryTreeNode

compareTo(Object) - Method in class baseCode.dataStructure.tree.TreeNode

computeRanking(AbstractNamedDoubleMatrix, AbstractNamedDoubleMatrix, int) - Method in class baseCode.algorithm.learning.unsupervised.RankProp

computeRanking(AbstractNamedDoubleMatrix, DoubleMatrix1D, int) - Method in class baseCode.algorithm.learning.unsupervised.RankProp

containsColumnName(String) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

containsColumnName(String) - Method in interface baseCode.dataStructure.matrix.NamedMatrix

containsKey(Object) - Method in class baseCode.dataStructure.graph.AbstractGraph

containsKey(Object) - Method in interface baseCode.dataStructure.graph.Graph

containsRowName(String) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

containsRowName(String) - Method in interface baseCode.dataStructure.matrix.NamedMatrix

containsSame(Collection, Collection) - Static method in class baseCode.util.RegressionTesting
Test whether two collections contain the same items.
containsSame(Object[], Object[]) - Static method in class baseCode.util.RegressionTesting
Test whether two object arrays contain the same items.
containsSame(double[], double[]) - Static method in class baseCode.util.RegressionTesting
Test whether two double arrays contain the same items in any order (tolerance is ZERO)
copy() - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
Make a copy of a matrix.
correlAsByte(double) - Static method in class baseCode.math.CorrelationStats

correlation(DoubleArrayList, double, DoubleArrayList, double) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the correlation of two data sequences.
correlation(DoubleArrayList, DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
Calculate the pearson correlation of two arrays.
correlationForPvalue(double, int) - Static method in class baseCode.math.CorrelationStats
Find the approximate correlation required to meet a particular pvalue.
correlationMatrix(AbstractNamedDoubleMatrix) - Static method in class baseCode.math.MatrixStats

correlationMatrix(AbstractNamedDoubleMatrix, double) - Static method in class baseCode.math.MatrixStats

correlationOfStandardized(double[], double[]) - Static method in class baseCode.math.Distance
Highly optimized implementation of the Pearson correlation.
correlationOfStandardized(DoubleArrayList, DoubleArrayList) - Static method in class baseCode.math.Distance
Like correlationofNormedFast, but takes DoubleArrayLists as inputs, handles missing values correctly, and does more error checking.
correlationTstat(double, int) - Static method in class baseCode.math.CorrelationStats
Compute the t-statistic associated with a Pearson correlation.
countsNormalize(AbstractNamedDoubleMatrix, double) - Static method in class baseCode.math.MatrixStats
Normalize a count matrix in place to be a transition matrix.
covariance(DoubleArrayList, DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the SAMPLE covariance of two data sequences.
createColorPalette(int, Color[]) - Method in class baseCode.gui.ColorMap
Allocates colors across a range.
createEmptyRow(int) - Method in class baseCode.io.reader.DoubleMatrixReader

createMatrix(List, int, int, List, List) - Method in class baseCode.io.reader.DoubleMatrixReader

createRowKeys() - Method in class baseCode.gui.ColorMatrix
To be able to sort the rows by an arbitrary key.
cumulate(DoubleArrayList) - Static method in class baseCode.math.Stats
Convert an array into a cumulative array.
cumulateRight(DoubleArrayList) - Static method in class baseCode.math.Stats
Convert an array into a cumulative array.
cv(DoubleArrayList) - Static method in class baseCode.math.Stats
Compute the coefficient of variation of an array (standard deviation / mean)

D

DARK_RED - Static variable in class baseCode.gui.ColorMap

DATA_EXTENSIONS - Static variable in class baseCode.util.FileTools

DEFAULT_DATA_EXTENSION - Static variable in class baseCode.util.FileTools

DEFAULT_IMAGE_EXTENSION - Static variable in class baseCode.util.FileTools

DEFAULT_XML_EXTENSION - Static variable in class baseCode.util.FileTools

DESCENDING - Static variable in class baseCode.gui.table.TableSorter

DataFileFilter - class baseCode.gui.file.DataFileFilter.

DataFileFilter() - Constructor for class baseCode.gui.file.DataFileFilter

DenseDoubleMatrix1D - class baseCode.dataStructure.matrix.DenseDoubleMatrix1D.
Use this class when fast iteration over the matrix is of primary interest.
DenseDoubleMatrix1D(int, double[], int, int) - Constructor for class baseCode.dataStructure.matrix.DenseDoubleMatrix1D

DenseDoubleMatrix1D(double[]) - Constructor for class baseCode.dataStructure.matrix.DenseDoubleMatrix1D

DenseDoubleMatrix1D(int) - Constructor for class baseCode.dataStructure.matrix.DenseDoubleMatrix1D

DenseDoubleMatrix2DNamed - class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed.
A matrix of doubles that knows about row and column names.
DenseDoubleMatrix2DNamed(double[][]) - Constructor for class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed

DenseDoubleMatrix2DNamed(int, int) - Constructor for class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed

DensityGenerator - interface baseCode.math.distribution.DensityGenerator.
An interface that describes a class that can produce values from a particular probability density.
DescriptiveWithMissing - class baseCode.math.DescriptiveWithMissing.
Mathematical functions for statistics that allow missing values without scotching the calculations.
DirectedGraph - class baseCode.dataStructure.graph.DirectedGraph.
A graph that contains DirectedGraphNodes.
DirectedGraph() - Constructor for class baseCode.dataStructure.graph.DirectedGraph

DirectedGraph(Set) - Constructor for class baseCode.dataStructure.graph.DirectedGraph

DirectedGraphNode - class baseCode.dataStructure.graph.DirectedGraphNode.
A graph node that has the concept of parents and children.
DirectedGraphNode(Object, Object, Graph) - Constructor for class baseCode.dataStructure.graph.DirectedGraphNode

Dirichlet - class baseCode.math.distribution.Dirichlet.

Dirichlet(DoubleArrayList, RandomEngine) - Constructor for class baseCode.math.distribution.Dirichlet

Distance - class baseCode.math.Distance.
Alternative distance and similarity metrics for vectors.
Distance() - Constructor for class baseCode.math.Distance

DistanceFactory - class baseCode.algorithm.learning.unsupervised.cluster.DistanceFactory.

DistanceFactory() - Constructor for class baseCode.algorithm.learning.unsupervised.cluster.DistanceFactory

Distanceable - class baseCode.common.Distanceable.
An object whose distance to other objects can be measured.
Distanceable() - Constructor for class baseCode.common.Distanceable

Distancer - interface baseCode.algorithm.learning.unsupervised.cluster.Distancer.

DoubleArrayToString(double[]) - Method in class baseCode.io.StringConverter
Convert a double array to a delimited string.
DoubleMatrix2DNamedFactory - class baseCode.dataStructure.matrix.DoubleMatrix2DNamedFactory.
Use this factory to create matrices of type selected at runtime.
DoubleMatrix2DNamedFactory() - Constructor for class baseCode.dataStructure.matrix.DoubleMatrix2DNamedFactory

DoubleMatrixReader - class baseCode.io.reader.DoubleMatrixReader.
Reader for DenseDoubleMatrix2DNamed.
DoubleMatrixReader() - Constructor for class baseCode.io.reader.DoubleMatrixReader

dbinom(double, double, double) - Static method in class baseCode.math.SpecFunc
See dbinom_raw.
dense(double[][]) - Static method in class baseCode.dataStructure.matrix.DoubleMatrix2DNamedFactory

dense(int, int) - Static method in class baseCode.dataStructure.matrix.DoubleMatrix2DNamedFactory

density(double) - Method in interface baseCode.math.distribution.DensityGenerator

density(double) - Method in class baseCode.math.distribution.UniformDensityComputer

dequeue() - Method in class baseCode.dataStructure.Queue
Deprecated.
dhyper(int, int, int, int) - Static method in class baseCode.math.SpecFunc
Ported from R (Catherine Loader)
distAlg - Variable in class baseCode.algorithm.learning.unsupervised.cluster.Cluster

distance(Distanceable, Distanceable) - Method in class baseCode.algorithm.learning.unsupervised.cluster.AverageLinkageDistancer

distance(Distanceable, Distanceable) - Method in interface baseCode.algorithm.learning.unsupervised.cluster.Distancer

distanceTo(Distanceable) - Method in class baseCode.algorithm.learning.unsupervised.cluster.Cluster

distanceTo(Distanceable) - Method in class baseCode.common.Distanceable

doubleArrayToBytes(double[]) - Method in class baseCode.io.ByteArrayConverter

drawColumnNames(Graphics) - Method in class baseCode.gui.JMatrixDisplay
Draws column names vertically (turned 90 degrees counter-clockwise)
drawMatrix(Graphics, boolean) - Method in class baseCode.gui.JMatrixDisplay
Gets called from #paintComponent and #saveImage
drawRowNames(Graphics) - Method in class baseCode.gui.JMatrixDisplay
Draws row names (horizontally)
drawVerticalString(Graphics, String, Font, int, int) - Static method in class baseCode.graphics.text.Util
Draws a string vertically, turned 90 degrees counter-clockwise.
draws(int) - Method in class baseCode.math.distribution.Dirichlet

durbinWatson(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
Durbin-Watson computation.

E

EMPTY - Static variable in class baseCode.gui.JGradientBar

enqueue(Object) - Method in class baseCode.dataStructure.Queue
Deprecated.
ensureCapacity(int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed

error(String, Exception) - Static method in class baseCode.gui.GuiUtil

error(String) - Static method in class baseCode.gui.GuiUtil

euclDistance(DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.Distance
Calculate the Euclidean distance between two vectors.

F

F - Static variable in class baseCode.dataFilter.AffymetrixProbeNameFilter
Filter probes that have the "_f_at" (family) tag.
F - Static variable in class baseCode.dataFilter.RowAffyNameFilter
Filter probes that have the "_f_at" (family) tag.
FileTools - class baseCode.util.FileTools.
Copyright (c) 2004 Columbia University
FileTools() - Constructor for class baseCode.util.FileTools

Filter - interface baseCode.dataFilter.Filter.
An interface representing the functionality of a class that can filter 2-d matrix-based data by row-oriented criteria.
filter(NamedMatrix) - Method in class baseCode.dataFilter.AffymetrixProbeNameFilter

filter(NamedMatrix) - Method in interface baseCode.dataFilter.Filter
Filter the data
filter(NamedMatrix) - Method in class baseCode.dataFilter.ItemLevelFilter

filter(NamedMatrix) - Method in class baseCode.dataFilter.RowAbsentFilter
The data is going to be filtered in accordance to strings in 'flags'.
filter(NamedMatrix) - Method in class baseCode.dataFilter.RowAffyNameFilter

filter(NamedMatrix) - Method in class baseCode.dataFilter.RowLevelFilter

filter(NamedMatrix) - Method in class baseCode.dataFilter.RowMissingFilter

filter(NamedMatrix) - Method in class baseCode.dataFilter.RowNameFilter
Filter according to row names.
finishButton - Variable in class baseCode.gui.Wizard

finishButton_actionPerformed(ActionEvent) - Method in class baseCode.gui.Wizard
Define what happens when the 'finish' button is pressed.
firePropertyChange(String, Object, Object) - Method in class baseCode.gui.table.JMatrixCellRenderer

firePropertyChange(String, boolean, boolean) - Method in class baseCode.gui.table.JMatrixCellRenderer

firePropertyChange(String, Object, Object) - Method in class baseCode.gui.table.JVerticalHeaderRenderer

firePropertyChange(String, boolean, boolean) - Method in class baseCode.gui.table.JVerticalHeaderRenderer

fisherCombineLogPvalues(DoubleArrayList) - Method in class baseCode.math.metaanalysis.MetaAnalysis
Fisher's method for combining p values (Cooper and Hedges 15-8)
fisherCombinePvalues(DoubleArrayList) - Method in class baseCode.math.metaanalysis.MetaAnalysis
Fisher's method for combining p values.
fisherTransform(double) - Static method in class baseCode.math.CorrelationStats
Compute the Fisher z transform of the Pearson correlation.
fisherTransform(DoubleArrayList) - Static method in class baseCode.math.CorrelationStats
Fisher-transform a list of correlations.
fisherTransformedSamplingVariance(double) - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
Equation 18-8 from CH.
fisherTransformedSamplingVariances(DoubleArrayList) - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
Run equation CH 18-8 on a list of sample sizes.
flowlayout1 - Variable in class baseCode.gui.Wizard

forEachNonZero(DoubleFunction) - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D
Apply the given function to each element non-zero element in the matrix.

G

G - Static variable in class baseCode.dataFilter.AffymetrixProbeNameFilter
Filter probes that have the "_g_at" (group) tag.
G - Static variable in class baseCode.dataFilter.RowAffyNameFilter
Filter probes that have the "_g_at" (group) tag.
GIF_EXTENSION - Static variable in class baseCode.util.FileTools

GOEntry - class baseCode.bio.GOEntry.

GOEntry(String, String, String, String) - Constructor for class baseCode.bio.GOEntry

GONames - class baseCode.bio.geneset.GONames.
Rea data from GO XML file, store in easy-to-use data structure.
GONames(String) - Constructor for class baseCode.bio.geneset.GONames

GONames(InputStream) - Constructor for class baseCode.bio.geneset.GONames

GOParser - class baseCode.xml.GOParser.
Read in the GO XML file provided by the Gene Ontology Consortium.
GOParser(InputStream) - Constructor for class baseCode.xml.GOParser

GOTermList - class baseCode.bio.GOTermList.

GOTermList() - Constructor for class baseCode.bio.GOTermList

GOTermProbability - class baseCode.bio.GOTermProbability.

GOTermProbability() - Constructor for class baseCode.bio.GOTermProbability

GREENRED_COLORMAP - Static variable in class baseCode.gui.ColorMap

GeneAnnotations - class baseCode.bio.geneset.GeneAnnotations.
Reads tab-delimited file to create maps of probes to classes, classes to probes, probes to genes, genes to probes.
GeneAnnotations(String, StatusViewer) - Constructor for class baseCode.bio.geneset.GeneAnnotations
This is for creating GeneAnnotations by reading from a file
GeneAnnotations(GeneAnnotations, Set) - Constructor for class baseCode.bio.geneset.GeneAnnotations
This is for creating GeneAnnotations by pruning a copy.
GeneAnnotations(InputStream, Set, StatusViewer) - Constructor for class baseCode.bio.geneset.GeneAnnotations
Make a new GeneAnnotations that only includes the probes in the parameter 'probes'.
GeneAnnotations(String, Set, StatusViewer) - Constructor for class baseCode.bio.geneset.GeneAnnotations

GeneSetMapTools - class baseCode.bio.geneset.GeneSetMapTools.
Methods to 'clean' a set of geneSets - to remove redundancies, for example.
GeneSetMapTools() - Constructor for class baseCode.bio.geneset.GeneSetMapTools

Graph - interface baseCode.dataStructure.graph.Graph.

GraphNode - interface baseCode.dataStructure.graph.GraphNode.

GroupMap - class baseCode.misc.GroupMap.
A data structure representing a map between items and a single set of keys.
GroupMap() - Constructor for class baseCode.misc.GroupMap

GuiUtil - class baseCode.gui.GuiUtil.
Little oft-used functions.
GuiUtil() - Constructor for class baseCode.gui.GuiUtil

geneSetExists(String) - Method in class baseCode.bio.geneset.GeneAnnotations
Returns true if the class is in the classToProbe map
geneSetSizeDistribution(GeneAnnotations, int, int, int) - Static method in class baseCode.bio.geneset.GeneSetMapTools

geneSetToRedundantMap() - Method in class baseCode.bio.geneset.GeneAnnotations

geometricMean(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the geometric mean of a data sequence.
get() - Method in class baseCode.dataStructure.Point

get(Object) - Method in class baseCode.dataStructure.graph.AbstractGraph
Retrieve a node by key.
get(Object) - Method in interface baseCode.dataStructure.graph.Graph

get(int, int) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix

get(int, int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed

get(int, int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed

get(int, int) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed

get(int, int) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed

getAllChildNodes() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
Get all the children of this node, recursively.
getAllParentNodes() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
Get all the parents of this node, recursively.
getAlpha() - Method in class baseCode.algorithm.learning.unsupervised.RankProp

getAspect() - Method in class baseCode.bio.GOEntry

getAspectForId(String) - Method in class baseCode.bio.geneset.GONames
Get the aspect (molecular_function etc) for an id.
getBsv() - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis

getBsv() - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis

getChildGraph() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
Get the subgraph starting from this node, including this node.
getChildKeys() - Method in class baseCode.dataStructure.graph.DirectedGraphNode

getChildNodes() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
Get the immediate children of this node.
getChildren(String) - Method in class baseCode.bio.geneset.GONames

getClassToProbes(String) - Method in class baseCode.bio.geneset.GeneAnnotations

getCol(int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
Return a copy of a given column.
getCol(int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
Return a copy of a given column.
getCol(int) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed

getColByName(String) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
Return a copy of a given column.
getColIndexByName(String) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

getColIndexByName(String) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
Get the index of a column by name.
getColName(int) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

getColName(int) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
Gte the column name for an index.
getColNames() - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

getColNames() - Method in interface baseCode.dataStructure.matrix.NamedMatrix

getColObj(int) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix

getColObj(int) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

getColObj(int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed

getColObj(int) - Method in interface baseCode.dataStructure.matrix.NamedMatrix

getColObj(int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed

getColObj(int) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed

getColObj(int) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed

getColor(int) - Method in class baseCode.gui.ColorMap

getColor(int, int) - Method in class baseCode.gui.ColorMatrix

getColor(int, int) - Method in class baseCode.gui.JMatrixDisplay

getColorMap() - Method in class baseCode.gui.JMatrixDisplay

getColorMatrix() - Method in class baseCode.gui.JMatrixDisplay

getColumnClass(int) - Method in class baseCode.gui.table.TableSorter

getColumnCount() - Method in class baseCode.gui.ColorMatrix

getColumnCount() - Method in class baseCode.gui.JMatrixDisplay

getColumnCount() - Method in class baseCode.gui.table.TableSorter

getColumnName(int) - Method in class baseCode.gui.ColorMatrix

getColumnName(int) - Method in class baseCode.gui.JMatrixDisplay

getColumnName(int) - Method in class baseCode.gui.table.TableSorter

getColumnNames() - Method in class baseCode.gui.ColorMatrix

getColumnNames() - Method in class baseCode.gui.JMatrixDisplay

getComparator(int) - Method in class baseCode.gui.table.TableSorter

getComparator(Class) - Method in class baseCode.gui.table.TableSorter

getCon() - Method in class baseCode.db.Handle

getContents() - Method in class baseCode.dataStructure.tree.BinaryTreeNode

getDefinition() - Method in class baseCode.dataStructure.OntologyEntry

getDescription() - Method in class baseCode.gui.file.DataFileFilter

getDescription() - Method in class baseCode.gui.file.ImageFileFilter

getDescription() - Method in class baseCode.gui.file.XMLFileFilter

getDisplayMax() - Method in class baseCode.gui.ColorMatrix

getDisplayMax() - Method in class baseCode.gui.JMatrixDisplay

getDisplayMin() - Method in class baseCode.gui.ColorMatrix

getDisplayMin() - Method in class baseCode.gui.JMatrixDisplay

getDisplayRange() - Method in class baseCode.gui.JMatrixDisplay

getDistancer() - Method in class baseCode.algorithm.learning.unsupervised.cluster.DistanceFactory

getE() - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis

getE() - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis

getElement() - Method in class baseCode.dataStructure.tree.TreeNode

getExtension(String) - Static method in class baseCode.util.FileTools
Returns the extension of a file.
getFirstChild() - Method in class baseCode.dataStructure.tree.TreeNode

getGONameMap() - Method in class baseCode.xml.GOParser
Get a simple Map that contains keys that are the GO ids, values are the names.
getGeneProbeList(String) - Method in class baseCode.bio.geneset.GeneAnnotations
Get a list of the probes that correspond to a particular gene.
getGeneSetByIndex(int) - Method in class baseCode.bio.geneset.GeneAnnotations
Get a class by an integer index i from the sorted list.
getGeneSetToGeneMap() - Method in class baseCode.bio.geneset.GeneAnnotations

getGeneSetToProbeMap() - Method in class baseCode.bio.geneset.GeneAnnotations

getGeneToGeneSetMap() - Method in class baseCode.bio.geneset.GeneAnnotations

getGeneToProbeList() - Method in class baseCode.bio.geneset.GeneAnnotations

getGraph() - Method in class baseCode.bio.geneset.GONames
Get the graph representation of the GO hierarchy.
getGraph() - Method in class baseCode.dataStructure.graph.AbstractGraphNode

getGraph() - Method in interface baseCode.dataStructure.graph.GraphNode

getGraph() - Method in class baseCode.xml.GOParser
Get the graph that was created.
getHeaderRendererIcon(int, int) - Method in class baseCode.gui.table.TableSorter

getId() - Method in class baseCode.dataStructure.OntologyEntry

getItem() - Method in class baseCode.dataStructure.graph.AbstractGraphNode
Get the actual contents of the node.
getItem() - Method in interface baseCode.dataStructure.graph.GraphNode

getItems() - Method in class baseCode.dataStructure.graph.AbstractGraph

getKey() - Method in class baseCode.dataStructure.graph.AbstractGraphNode
Get the key for the node.
getKey() - Method in interface baseCode.dataStructure.graph.GraphNode

getLeft() - Method in class baseCode.dataStructure.tree.BinaryTree

getLeft() - Method in class baseCode.dataStructure.tree.BinaryTreeNode

getMap() - Method in class baseCode.bio.geneset.GONames
Get the Map representation of the GO id - name associations.
getMatrix() - Method in class baseCode.gui.ColorMatrix

getMatrix() - Method in class baseCode.gui.JMatrixDisplay

getMax() - Method in class baseCode.gui.JMatrixDisplay

getMaxIter() - Method in class baseCode.algorithm.learning.unsupervised.RankProp
Maximum iterations before stopping.
getMin() - Method in class baseCode.gui.JMatrixDisplay

getMissingColor() - Method in class baseCode.gui.JMatrixDisplay

getN() - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis

getN() - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis

getName() - Method in class baseCode.dataStructure.OntologyEntry

getNameForId(String) - Method in class baseCode.bio.geneset.GONames

getNewGeneSets() - Method in class baseCode.bio.geneset.GONames
Return the Set of all new gene sets (ones which were added after loading the file)
getNextSibling() - Method in class baseCode.dataStructure.tree.TreeNode

getNodeContents(Object) - Method in class baseCode.dataStructure.graph.AbstractGraph
Retrieve the contents of a node by key.
getNodeContents(Object) - Method in interface baseCode.dataStructure.graph.Graph

getOutputMatrix(NamedMatrix, int, int) - Method in class baseCode.dataFilter.AbstractFilter

getP() - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis

getP() - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis

getPalette() - Method in class baseCode.gui.ColorMap

getPaletteSize() - Method in class baseCode.gui.ColorMap

getParentKeys() - Method in class baseCode.dataStructure.graph.DirectedGraphNode

getParentNodes() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
Get the immediate parents of this node.
getParents(String) - Method in class baseCode.bio.geneset.GONames

getPreferredSize() - Method in class baseCode.gui.table.JVerticalHeaderRenderer

getProbeDescription(String) - Method in class baseCode.bio.geneset.GeneAnnotations
Get the description for a gene.
getProbeGeneName(String) - Method in class baseCode.bio.geneset.GeneAnnotations
Get the gene that a probe belongs to.
getProbeToGeneMap() - Method in class baseCode.bio.geneset.GeneAnnotations

getProbeToGeneSetMap() - Method in class baseCode.bio.geneset.GeneAnnotations

getQ() - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis

getQ() - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis

getQuick(int, int) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix

getQuick(int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix1D
This is an optimized version of getQuick.
getQuick(int, int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed

getQuick(int) - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D

getQuick(int, int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed

getQuick(int, int) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed

getQuick(int, int) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed

getRedundancies(String, Map) - Static method in class baseCode.bio.geneset.GeneSetMapTools

getRedundanciesString(String, Map) - Method in class baseCode.bio.geneset.GeneSetMapTools

getResults() - Method in class baseCode.algorithm.learning.unsupervised.cluster.HierarchicalClusterer

getRight() - Method in class baseCode.dataStructure.tree.BinaryTree

getRight() - Method in class baseCode.dataStructure.tree.BinaryTreeNode

getRoot() - Method in class baseCode.dataStructure.tree.BinaryTree

getRow(int) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix

getRow(int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
Return a reference to a specific row.
getRow(int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed
Return a reference to a specific row.
getRow(int) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed

getRow(int) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed

getRow(int) - Method in class baseCode.gui.ColorMatrix

getRow(int) - Method in class baseCode.gui.JMatrixDisplay

getRowArrayList(int) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix

getRowArrayList(int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed

getRowArrayList(int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed

getRowArrayList(int) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
This gives just the list of values in the row - make sure this is what you want.
getRowByName(String) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix

getRowByName(String) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
Return a reference to a specific row.
getRowByName(String) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed

getRowByName(String) - Method in class baseCode.gui.ColorMatrix

getRowByName(String) - Method in class baseCode.gui.JMatrixDisplay

getRowCount() - Method in class baseCode.gui.ColorMatrix

getRowCount() - Method in class baseCode.gui.JMatrixDisplay

getRowCount() - Method in class baseCode.gui.table.TableSorter

getRowHeight() - Method in class baseCode.gui.JMatrixDisplay

getRowIndexByName(String) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

getRowIndexByName(String) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
Get the index of a row by name..
getRowIndexByName(String) - Method in class baseCode.gui.ColorMatrix

getRowIndexByName(String) - Method in class baseCode.gui.JMatrixDisplay

getRowName(int) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

getRowName(int) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
Get the row name for an index
getRowName(int) - Method in class baseCode.gui.ColorMatrix

getRowName(int) - Method in class baseCode.gui.JMatrixDisplay

getRowNameMapIterator() - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

getRowNameMapIterator() - Method in interface baseCode.dataStructure.matrix.NamedMatrix

getRowNames() - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

getRowNames() - Method in interface baseCode.dataStructure.matrix.NamedMatrix

getRowNames() - Method in class baseCode.gui.ColorMatrix

getRowNames() - Method in class baseCode.gui.JMatrixDisplay

getRowObj(int) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix

getRowObj(int) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

getRowObj(int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed

getRowObj(int) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
Get a row in the matrix as a generic Object[].
getRowObj(int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed

getRowObj(int) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed

getRowObj(int) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed

getScores() - Method in class baseCode.algorithm.Ranker

getSelectedProbes() - Method in class baseCode.bio.geneset.GeneAnnotations

getSelectedSets() - Method in class baseCode.bio.geneset.GeneAnnotations

getSimilarities(String, Map) - Static method in class baseCode.bio.geneset.GeneSetMapTools

getSize(boolean) - Method in class baseCode.gui.JMatrixDisplay

getSortingStatus(int) - Method in class baseCode.gui.table.TableSorter

getStandardizedEnabled() - Method in class baseCode.gui.JMatrixDisplay

getStepSize(int, int, int) - Method in class baseCode.gui.ColorMap
Calculate how fast we have to change color components.
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class baseCode.gui.table.JBarGraphCellRenderer
This method is called each time a cell in a column using this renderer needs to be rendered.
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class baseCode.gui.table.JMatrixCellRenderer

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class baseCode.gui.table.JVerticalHeaderRenderer

getTableHeader() - Method in class baseCode.gui.table.TableSorter

getTableModel() - Method in class baseCode.gui.table.TableSorter

getTopoSortOrder() - Method in class baseCode.dataStructure.graph.DirectedGraphNode

getTrueRowIndex(int) - Method in class baseCode.gui.ColorMatrix

getURL() - Method in class baseCode.gui.JLinkLabel

getUniqueItems() - Method in class baseCode.misc.GroupMap

getV() - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis

getV() - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis

getValue(int, int) - Method in class baseCode.gui.ColorMatrix

getValue(int, int) - Method in class baseCode.gui.JMatrixDisplay

getValueAt(int, int) - Method in class baseCode.gui.table.TableSorter

getWeight() - Method in class baseCode.dataStructure.Link

getWithoutExtension(String) - Static method in class baseCode.util.FileTools

getZ() - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis

getZ() - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis

getx() - Method in class baseCode.dataStructure.Point

gety() - Method in class baseCode.dataStructure.Point

graph - Variable in class baseCode.dataStructure.graph.AbstractGraphNode

H

Handle - class baseCode.db.Handle.
Database handle container and query convenience functions.
Handle(String, String, String, String) - Constructor for class baseCode.db.Handle

Handle() - Constructor for class baseCode.db.Handle

Handle(String, String) - Constructor for class baseCode.db.Handle

HierarchicalClusterer - class baseCode.algorithm.learning.unsupervised.cluster.HierarchicalClusterer.
Start with all items in separate clusters.
HierarchicalClusterer(ObjectArrayList) - Constructor for class baseCode.algorithm.learning.unsupervised.cluster.HierarchicalClusterer

HistogramWriter - class baseCode.io.writer.HistogramWriter.
Print an hep.aidia.IHistogram1Dobject to a text file.
HistogramWriter() - Constructor for class baseCode.io.writer.HistogramWriter

hasChild(Object) - Method in class baseCode.dataStructure.graph.DirectedGraphNode
Check to see if this node has a particular immediate child.
hasColNames() - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

hasColNames() - Method in interface baseCode.dataStructure.matrix.NamedMatrix
Check if this matrix has a valid set of column names.
hasDataExtension(String) - Static method in class baseCode.util.FileTools

hasDuplicates(String) - Method in class baseCode.misc.GroupMap
For a given key, return true if it has duplicates.
hasImageExtension(String) - Static method in class baseCode.util.FileTools

hasParent(Object) - Method in class baseCode.dataStructure.graph.DirectedGraphNode
Check to see if this node has a particular immediate parent.
hasRow(String) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

hasRow(String) - Method in interface baseCode.dataStructure.matrix.NamedMatrix

hasRowNames() - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

hasRowNames() - Method in interface baseCode.dataStructure.matrix.NamedMatrix

hasXMLExtension(String) - Static method in class baseCode.util.FileTools

helpButton - Variable in class baseCode.gui.AppDialog

helpButton_actionPerformed(ActionEvent) - Method in class baseCode.gui.AppDialog

highCut - Variable in class baseCode.dataFilter.AbstractLevelFilter

hyperlinkUpdate(HyperlinkEvent) - Method in class baseCode.gui.JWebBrowser

I

IMAGE_EXTENSIONS - Static variable in class baseCode.util.FileTools

ImageFileFilter - class baseCode.gui.file.ImageFileFilter.

ImageFileFilter() - Constructor for class baseCode.gui.file.ImageFileFilter

ItemLevelFilter - class baseCode.dataFilter.ItemLevelFilter.
Filter that remove individual values that are outside of a range.
ItemLevelFilter() - Constructor for class baseCode.dataFilter.ItemLevelFilter

ignoreSimilar(double, GeneAnnotations, StatusViewer, int, int, double) - Static method in class baseCode.bio.geneset.GeneSetMapTools
Remove classes which are too similar to some other class.
inDegree() - Method in class baseCode.dataStructure.graph.DirectedGraphNode

incrementalUpdate(DoubleArrayList, int, int, double[]) - Static method in class baseCode.math.DescriptiveWithMissing
Not supported.
incrementalUpdateSumsOfPowers(DoubleArrayList, int, int, int, int, double[]) - Static method in class baseCode.math.DescriptiveWithMissing
Not supported.
incrementalWeightedUpdate(DoubleArrayList, DoubleArrayList, int, int, double[]) - Static method in class baseCode.math.DescriptiveWithMissing
Not supported.
indexes - Variable in class baseCode.dataStructure.matrix.RCDoubleMatrix1D

init(AbstractNamedDoubleMatrix) - Method in class baseCode.gui.ColorMatrix

init(ColorMatrix) - Method in class baseCode.gui.JMatrixDisplay

init(long) - Static method in class baseCode.math.RandomChooser
Initialized the random number generator witha given seed.
initSize() - Method in class baseCode.gui.JMatrixDisplay
Sets the display size
insertLeft(BinaryTreeNode, Object) - Method in class baseCode.dataStructure.tree.BinaryTree

insertRight(BinaryTreeNode, Object) - Method in class baseCode.dataStructure.tree.BinaryTree

intArrayToBytes(int[]) - Method in class baseCode.io.ByteArrayConverter

isCellEditable(int, int) - Method in class baseCode.gui.table.TableSorter

isCompound() - Method in class baseCode.algorithm.learning.unsupervised.cluster.Cluster

isEmpty() - Method in class baseCode.dataStructure.Queue
Deprecated.
isEmpty() - Method in class baseCode.dataStructure.Stack
Deprecated.
isEmpty() - Method in class baseCode.dataStructure.tree.BinaryTree

isFull() - Method in class baseCode.dataStructure.Queue
Deprecated.
isFull() - Method in class baseCode.dataStructure.Stack
Deprecated.
isLeaf() - Method in class baseCode.dataStructure.graph.DirectedGraphNode

isLeaf() - Method in class baseCode.dataStructure.tree.BinaryTreeNode

isMissing(int, int) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix

isMissing(int, int) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

isMissing(int, int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed

isMissing(int, int) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
Check if the value at a given index is missing.
isMissing(int, int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed

isMissing(int, int) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
(non-Javadoc) Note that in a sparse matrix, zero values are considered "missing"!
isMissing(int, int) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed

isReady() - Method in class baseCode.gui.WizardStep

isSorting() - Method in class baseCode.gui.table.TableSorter

isValidFraction(double) - Static method in class baseCode.math.Stats
Test whether a value is a valid fractional or probability value.
isValidPearsonCorrelation(double) - Static method in class baseCode.math.CorrelationStats
Test if a value is a reasonable Pearson correlation (in the range -1 to 1; values outside of this range are acceptable within a small roundoff.
isVisited() - Method in class baseCode.common.Visitable

isVisited() - Method in class baseCode.dataStructure.graph.AbstractGraphNode

item - Variable in class baseCode.dataStructure.graph.AbstractGraphNode

items - Variable in class baseCode.algorithm.learning.unsupervised.cluster.Cluster

items - Variable in class baseCode.dataStructure.graph.AbstractGraph

J

JBarGraphCellRenderer - class baseCode.gui.table.JBarGraphCellRenderer.

JBarGraphCellRenderer() - Constructor for class baseCode.gui.table.JBarGraphCellRenderer

JGradientBar - class baseCode.gui.JGradientBar.
A GUI legend component that displays a color map as a color gradient from min to max, traversing all the colors in the color map.
JGradientBar() - Constructor for class baseCode.gui.JGradientBar
Creates a new instance of JGradientBar
JLinkLabel - class baseCode.gui.JLinkLabel.
A clickable link label that contains a URL.
JLinkLabel() - Constructor for class baseCode.gui.JLinkLabel
Creates a new instance of JLinkLabel
JLinkLabel(String) - Constructor for class baseCode.gui.JLinkLabel

JLinkLabel(String, String) - Constructor for class baseCode.gui.JLinkLabel

JMatrixCellRenderer - class baseCode.gui.table.JMatrixCellRenderer.

JMatrixCellRenderer(JMatrixDisplay) - Constructor for class baseCode.gui.table.JMatrixCellRenderer

JMatrixDisplay - class baseCode.gui.JMatrixDisplay.
Title: JMatrixDisplay
JMatrixDisplay(String) - Constructor for class baseCode.gui.JMatrixDisplay

JMatrixDisplay(DenseDoubleMatrix2DNamed) - Constructor for class baseCode.gui.JMatrixDisplay

JMatrixDisplay(ColorMatrix) - Constructor for class baseCode.gui.JMatrixDisplay

JVerticalHeaderRenderer - class baseCode.gui.table.JVerticalHeaderRenderer.

JVerticalHeaderRenderer() - Constructor for class baseCode.gui.table.JVerticalHeaderRenderer

JWebBrowser - class baseCode.gui.JWebBrowser.

JWebBrowser(String) - Constructor for class baseCode.gui.JWebBrowser

jLabelStatus - Variable in class baseCode.gui.Wizard

jPanelStatus - Variable in class baseCode.gui.Wizard

jbInit() - Method in class baseCode.gui.WizardStep

K

KSTest - class baseCode.math.KSTest.
Class to perform the Kolmogorov-Smirnov test.
KSTest() - Constructor for class baseCode.math.KSTest

key - Variable in class baseCode.dataStructure.graph.AbstractGraphNode

kurtosis(double, double) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the kurtosis (aka excess) of a data sequence.
kurtosis(DoubleArrayList, double, double) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the kurtosis (aka excess) of a data sequence, which is -3 + moment(data,4,mean) / standardDeviation⁴.

L

LEXICAL_COMPARATOR - Static variable in class baseCode.gui.table.TableSorter

LINE_WIDTH - Static variable in class baseCode.gui.table.JBarGraphCellRenderer

Link - class baseCode.dataStructure.Link.
Title:
Link(int, int, double) - Constructor for class baseCode.dataStructure.Link

lag1(DoubleArrayList, double) - Static method in class baseCode.math.DescriptiveWithMissing
Not supported.
like(int) - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D

like2D(int, int) - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D

loadMatrixFromFile(String) - Method in class baseCode.gui.ColorMatrix
A convenience method for loading data files
log - Static variable in class baseCode.algorithm.Algorithm

log - Static variable in class baseCode.dataFilter.AbstractFilter

log - Static variable in class baseCode.dataStructure.graph.AbstractGraphNode

log - Static variable in class baseCode.gui.GuiUtil

log - Static variable in class baseCode.io.reader.AbstractNamedMatrixReader

log - Static variable in class baseCode.util.StatusDebugLogger

lowCut - Variable in class baseCode.dataFilter.AbstractLevelFilter

M

MAX - Static variable in class baseCode.dataFilter.RowLevelFilter
Use the maximum of the row as the criterion.
MEAN - Static variable in class baseCode.dataFilter.RowLevelFilter
Use the mean as the criterion.
MEDIAN - Static variable in class baseCode.dataFilter.RowLevelFilter
Use the median as the criterion.
MIN - Static variable in class baseCode.dataFilter.RowLevelFilter
Use the minimum of the row as the criterion.
M_1_PI - Static variable in class baseCode.math.Constants

M_1_SQRT_2 - Static variable in class baseCode.math.Constants

M_1_SQRT_2PI - Static variable in class baseCode.math.Constants

M_LN_2 - Static variable in class baseCode.math.Constants

M_LN_SQRT_2PI - Static variable in class baseCode.math.Constants

M_LN_SQRT_PI - Static variable in class baseCode.math.Constants

M_LN_SQRT_PId2 - Static variable in class baseCode.math.Constants

M_LOG10_2 - Static variable in class baseCode.math.Constants

M_PI_2 - Static variable in class baseCode.math.Constants

M_PI_4 - Static variable in class baseCode.math.Constants

M_PI_half - Static variable in class baseCode.math.Constants

M_SQRT_2 - Static variable in class baseCode.math.Constants

M_SQRT_2dPI - Static variable in class baseCode.math.Constants

M_SQRT_PI - Static variable in class baseCode.math.Constants

MapReader - class baseCode.io.reader.MapReader.
Reads a tab-delimited file with lines of the format Key Value.
MapReader() - Constructor for class baseCode.io.reader.MapReader

MatrixRowStats - class baseCode.math.MatrixRowStats.
Convenience functions for getting row statistics from matrices.
MatrixStats - class baseCode.math.MatrixStats.

MatrixStats() - Constructor for class baseCode.math.MatrixStats

MeanDifferenceMetaAnalysis - class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis.
Meta-analysis methods from chapter 18 of Cooper and Hedges, sections 2.1 and 3.1
MeanDifferenceMetaAnalysis(boolean) - Constructor for class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis

MetaAnalysis - class baseCode.math.metaanalysis.MetaAnalysis.
Statistics for meta-analysis.
MetaAnalysis() - Constructor for class baseCode.math.metaanalysis.MetaAnalysis

MultipleTestCorrection - class baseCode.math.MultipleTestCorrection.
Methods for p-value correction of sets of hypothesis tests.
MultipleTestCorrection() - Constructor for class baseCode.math.MultipleTestCorrection

m_cellSize - Variable in class baseCode.gui.JMatrixDisplay

m_colorMap - Variable in class baseCode.gui.ColorMatrix

m_colorPalette - Variable in class baseCode.gui.ColorMap

m_colors - Variable in class baseCode.gui.ColorMatrix

m_columnLabelHeight - Variable in class baseCode.gui.JMatrixDisplay

m_currentColorMap - Variable in class baseCode.gui.ColorMap

m_customColorMap - Variable in class baseCode.gui.ColorMap

m_defaultResolution - Variable in class baseCode.gui.JMatrixDisplay

m_defaultSuggestedNumberOfColors - Static variable in class baseCode.gui.ColorMap

m_displayMax - Variable in class baseCode.gui.ColorMatrix

m_displayMin - Variable in class baseCode.gui.ColorMatrix
Min and max values to display, which might not be the actual min and max values in the matrix.
m_fontGutter - Variable in class baseCode.gui.JMatrixDisplay

m_fontSize - Variable in class baseCode.gui.JMatrixDisplay

m_gradient - Variable in class baseCode.gui.JGradientBar

m_image - Variable in class baseCode.gui.JMatrixDisplay

m_isBarGraph - Variable in class baseCode.gui.table.JBarGraphCellRenderer

m_isSelected - Variable in class baseCode.gui.table.JBarGraphCellRenderer

m_isShowLabels - Variable in class baseCode.gui.JMatrixDisplay

m_labelFont - Variable in class baseCode.gui.JMatrixDisplay

m_labelGutter - Variable in class baseCode.gui.JMatrixDisplay

m_matrix - Variable in class baseCode.gui.ColorMatrix

m_matrixReader - Variable in class baseCode.gui.ColorMatrix

m_max - Variable in class baseCode.gui.ColorMatrix

m_max - Variable in class baseCode.gui.JGradientBar

m_maxColor - Variable in class baseCode.gui.ColorMap
last color in the current color map
m_maxFontSize - Variable in class baseCode.gui.JMatrixDisplay

m_min - Variable in class baseCode.gui.ColorMatrix

m_min - Variable in class baseCode.gui.JGradientBar

m_minColor - Variable in class baseCode.gui.ColorMap
first color in the current color map
m_missingColor - Variable in class baseCode.gui.ColorMatrix

m_noFocusBorder - Static variable in class baseCode.gui.table.JBarGraphCellRenderer

m_ratioWidth - Variable in class baseCode.gui.JMatrixDisplay

m_resolution - Variable in class baseCode.gui.JMatrixDisplay

m_rowKeys - Variable in class baseCode.gui.ColorMatrix
to be able to sort the rows by an arbitrary key
m_rowLabelWidth - Variable in class baseCode.gui.JMatrixDisplay

m_selectionBackground - Static variable in class baseCode.gui.table.JBarGraphCellRenderer

m_text - Variable in class baseCode.gui.JLinkLabel

m_textSize - Variable in class baseCode.gui.JMatrixDisplay

m_totalColumns - Variable in class baseCode.gui.ColorMatrix

m_totalRows - Variable in class baseCode.gui.ColorMatrix

m_url - Variable in class baseCode.gui.JLinkLabel

m_values - Variable in class baseCode.gui.table.JBarGraphCellRenderer

main(String[]) - Static method in class baseCode.gui.JWebBrowser

mainPanel - Variable in class baseCode.gui.Wizard

makeEmpty() - Method in class baseCode.dataStructure.Queue
Deprecated.
manhattanDistance(DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.Distance
Calculate the Manhattan distance between two vectors.
mapValuesToColors() - Method in class baseCode.gui.ColorMatrix

mark() - Method in class baseCode.common.Visitable

mark() - Method in class baseCode.dataStructure.graph.AbstractGraphNode

max(AbstractNamedDoubleMatrix) - Static method in class baseCode.math.MatrixStats
Compute the maximum value in the matrix.
maxStringPixelWidth(String[], Font, Component) - Static method in class baseCode.graphics.text.Util

mean(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing

mean(DoubleArrayList, int) - Static method in class baseCode.math.DescriptiveWithMissing
Special mean calculation where we use the effective size as an input.
mean(double[], int) - Static method in class baseCode.math.DescriptiveWithMissing
Special mean calculation where we use the effective size as an input.
meanAboveQuantile(int, DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
Calculate the mean of the values above a particular quantile of an array.
meanAboveQuantile(int, double[], int) - Static method in class baseCode.math.Stats
calculate the mean of the values above (NOT greater or equal to) a particular index rank of an array.
meanGeneSetSize(GeneAnnotations, boolean) - Static method in class baseCode.bio.geneset.GeneSetMapTools

meanSetsPerGene(GeneAnnotations, boolean) - Static method in class baseCode.bio.geneset.GeneSetMapTools

means(DenseDoubleMatrix2DNamed) - Static method in class baseCode.math.MatrixRowStats
Calculates the means of a matrix's rows.
median(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the median of a sorted data sequence.
metaFEWeights(DoubleArrayList) - Method in class baseCode.math.metaanalysis.MetaAnalysis
Weights under a fixed effects model.
metaRESampleVariance(DoubleArrayList) - Method in class baseCode.math.metaanalysis.MetaAnalysis
CH sample variance under random effects model, equation 18-20
metaREVariance(DoubleArrayList, DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.metaanalysis.MetaAnalysis
CH equation 18-23.
metaREWeights(DoubleArrayList, double) - Method in class baseCode.math.metaanalysis.MetaAnalysis
Under a random effects model, CH eqn.
metaVariance(DoubleArrayList) - Method in class baseCode.math.metaanalysis.MetaAnalysis
CH 18-3.
metaVariance(DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.metaanalysis.MetaAnalysis
CH 18-3 version 2 for quality weighted.
metaZscore(double, double) - Method in class baseCode.math.metaanalysis.MetaAnalysis
Test statistic for H0: effectSize == 0.
min(AbstractNamedDoubleMatrix) - Static method in class baseCode.math.MatrixStats
Find the minimum of the entire matrix.
modelIndex(int) - Method in class baseCode.gui.table.TableSorter

modifyClass(String, String) - Method in class baseCode.bio.geneset.GONames

modifyClass(String, ArrayList) - Method in class baseCode.bio.geneset.GeneAnnotations
Redefine a class.
moment(DoubleArrayList, int, double) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the moment of k -th order with constant c of a data sequence, which is Sum( (data[i]-c)^k ) / data.size().
mouseButton_actionPerformed(MouseEvent) - Method in class baseCode.gui.AppDialog

mouseClicked(MouseEvent) - Method in class baseCode.gui.JLinkLabel

mouseEntered(MouseEvent) - Method in class baseCode.gui.JLinkLabel

mouseExited(MouseEvent) - Method in class baseCode.gui.JLinkLabel

mousePressed(MouseEvent) - Method in class baseCode.gui.JLinkLabel

mouseReleased(MouseEvent) - Method in class baseCode.gui.JLinkLabel

N

NOT_SORTED - Static variable in class baseCode.gui.table.TableSorter

NamedMatrix - interface baseCode.dataStructure.matrix.NamedMatrix.
Copyright (c) 2004
NormalProbabilityComputer - class baseCode.math.distribution.NormalProbabilityComputer.

NormalProbabilityComputer(double, double) - Constructor for class baseCode.math.distribution.NormalProbabilityComputer

newSet(String) - Method in class baseCode.bio.geneset.GONames
Check if a gene set is already defined.
newStatement() - Method in class baseCode.db.Handle

nextButton - Variable in class baseCode.gui.Wizard

nextButton_actionPerformed(ActionEvent) - Method in class baseCode.gui.Wizard
Define what happens when the 'next' button is pressed
nextDouble() - Method in class baseCode.math.distribution.Dirichlet

nextDoubleMatrix() - Method in class baseCode.math.distribution.Wishart
Based on R code from Francesca Dominici, http://www.biostat.jhsph.edu/~fdominic/teaching/BM/bm.html
normalize(DoubleArrayList, double) - Static method in class baseCode.math.Stats
Divide the elements of an array by a given factor.
normalize(DoubleArrayList) - Static method in class baseCode.math.Stats
Adjust the elements of an array so they total to 1.0.
numAnnotatedGenes() - Method in class baseCode.bio.geneset.GeneAnnotations
Compute how many genes have Gene set annotations.
numChildren() - Method in class baseCode.dataStructure.graph.DirectedGraphNode

numDuplicates(String) - Method in class baseCode.misc.GroupMap
For a given key, return the number of duplicates it has (not counting itself).
numGeneSets() - Method in class baseCode.bio.geneset.GeneAnnotations
Get the number of classes.
numGenes() - Method in class baseCode.bio.geneset.GeneAnnotations
How many genes are in the file?
numGenesInGeneSet(String) - Method in class baseCode.bio.geneset.GeneAnnotations
Get the number of genes in a gene set, identified by id.
numMissing() - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

numMissing() - Method in interface baseCode.dataStructure.matrix.NamedMatrix
Return the number of missing values in the matrix.
numNeighbors() - Method in class baseCode.dataStructure.graph.UndirectedGraphNode

numParents() - Method in class baseCode.dataStructure.graph.DirectedGraphNode

numProbesForGene(String) - Method in class baseCode.bio.geneset.GeneAnnotations
Get how many probes point to the same gene.
numProbesInGeneSet(String) - Method in class baseCode.bio.geneset.GeneAnnotations
Get the number of probes in a gene set, identified by id.

O

OntologyEntry - class baseCode.dataStructure.OntologyEntry.
A class representing a descriptive term that can be associated with things.
OntologyEntry(String) - Constructor for class baseCode.dataStructure.OntologyEntry

OntologyEntry(String, String, String) - Constructor for class baseCode.dataStructure.OntologyEntry

oneSample(DoubleArrayList, ProbabilityComputer) - Static method in class baseCode.math.KSTest

openURL(String) - Static method in class baseCode.util.BrowserLauncher
Attempts to open the default web browser to the given URL.
order(DoubleArrayList) - Static method in class baseCode.math.Rank
Return a permutation which puts the array in sorted order.
outDegree() - Method in class baseCode.dataStructure.graph.DirectedGraphNode

P

PNG_EXTENSION - Static variable in class baseCode.util.FileTools

Point - class baseCode.dataStructure.Point.
Title:
Point(int, int) - Constructor for class baseCode.dataStructure.Point

ProbabilityComputer - interface baseCode.math.distribution.ProbabilityComputer.
An interface that describes objects that can produce probabilities according to some distribution.
paintBackground(Graphics) - Method in class baseCode.gui.table.JBarGraphCellRenderer

paintComponent(Graphics) - Method in class baseCode.gui.JMatrixDisplay
JComponent method used to render this component
paintComponent(Graphics) - Method in class baseCode.gui.table.JBarGraphCellRenderer

paintComponent(Graphics) - Method in class baseCode.gui.table.JVerticalHeaderRenderer

parents - Variable in class baseCode.dataStructure.graph.DirectedGraphNode

phyper(int, int, int, int, boolean) - Static method in class baseCode.math.SpecFunc
Ported from R phyper.c
pop() - Method in class baseCode.dataStructure.Stack
Deprecated. Remove the most recently added item.
prepareStatement(String) - Method in class baseCode.db.Handle

print(Writer) - Method in class baseCode.bio.geneset.GeneAnnotations
Print out the gene annotations in the same format we got them in, but if the gene sets have been modified, this will be reflected.
probability(double) - Method in class baseCode.math.distribution.NormalProbabilityComputer

probability(double, boolean) - Method in class baseCode.math.distribution.NormalProbabilityComputer

probability(double) - Method in interface baseCode.math.distribution.ProbabilityComputer
Return the probability associated with a certain value.The upper tail of the associated distribution is returned.
probability(double, boolean) - Method in interface baseCode.math.distribution.ProbabilityComputer
Return the probability associated with a certain value, with choice of tail.
probability(double) - Method in class baseCode.math.distribution.UniformProbabilityComputer

probability(double, boolean) - Method in class baseCode.math.distribution.UniformProbabilityComputer

product(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the product of a data sequence, which is Prod( data[i] ).
prune() - Method in class baseCode.dataStructure.graph.DirectedGraph
Remove vertices to nodes that aren't in the graph.
prune() - Method in class baseCode.dataStructure.graph.DirectedGraphNode
Remove connections that are to nodes not contained in this graph
push(Object) - Method in class baseCode.dataStructure.Stack
Deprecated. Add an item to the stack.
pvalue(double, int) - Static method in class baseCode.math.CorrelationStats

pvalueAsByte(double, int) - Static method in class baseCode.math.CorrelationStats
Conver a correlation p value into a value between 0 and 255 inclusive.

Q

Queue - class baseCode.dataStructure.Queue.
Deprecated. -- use java.util.List instead.
Queue() - Constructor for class baseCode.dataStructure.Queue
Deprecated.
Queue(int) - Constructor for class baseCode.dataStructure.Queue
Deprecated.
qStatistic(DoubleArrayList, DoubleArrayList, double) - Method in class baseCode.math.metaanalysis.MetaAnalysis
The "Q" statistic used to test homogeneity of effect sizes.
qTest(double, double) - Method in class baseCode.math.metaanalysis.MetaAnalysis
Test for statistical significance of Q.
quantile(DoubleArrayList, double) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the phi- quantile; that is, an element elem for which holds that phi percent of data elements are less than elem.
quantile(int, double[], int) - Static method in class baseCode.math.Stats
Given a double array, calculate the quantile requested.
quantileInverse(DoubleArrayList, double) - Static method in class baseCode.math.DescriptiveWithMissing
Returns how many percent of the elements contained in the receiver are <= element.
quantiles(DoubleArrayList, DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the quantiles of the specified percentages.
queryToDouble(String) - Method in class baseCode.db.Handle

queryToInt(String) - Method in class baseCode.db.Handle

queryToList(String) - Method in class baseCode.db.Handle

queryToMap(String) - Method in class baseCode.db.Handle

queryToSet(String) - Method in class baseCode.db.Handle

queryToString(String) - Method in class baseCode.db.Handle

quote(String) - Method in class baseCode.db.Handle

R

RANGE - Static variable in class baseCode.dataFilter.RowLevelFilter
Use the range as the criterion
RCDoubleMatrix1D - class baseCode.dataStructure.matrix.RCDoubleMatrix1D.
A row-compressed 1D matrix.
RCDoubleMatrix1D(double[]) - Constructor for class baseCode.dataStructure.matrix.RCDoubleMatrix1D

RCDoubleMatrix1D(int) - Constructor for class baseCode.dataStructure.matrix.RCDoubleMatrix1D

RCDoubleMatrix1D(IntArrayList, DoubleArrayList) - Constructor for class baseCode.dataStructure.matrix.RCDoubleMatrix1D

REDGREEN_COLORMAP - Static variable in class baseCode.gui.ColorMap

ROC - class baseCode.math.ROC.
Functions for calculating Receiver operator characteristics.
ROC() - Constructor for class baseCode.math.ROC

RandomChooser - class baseCode.math.RandomChooser.
Fill arrays with random values given a source of values.
Rank - class baseCode.math.Rank.
Calculate rank statistics for arrays.
Rank() - Constructor for class baseCode.math.Rank

RankProp - class baseCode.algorithm.learning.unsupervised.RankProp.
Implementation of RankProp, as described in Weston et al.
RankProp() - Constructor for class baseCode.algorithm.learning.unsupervised.RankProp

Ranker - class baseCode.algorithm.Ranker.

Ranker() - Constructor for class baseCode.algorithm.Ranker

RegressionTesting - class baseCode.util.RegressionTesting.
Tools to help make regression testing easier.
RowAbsentFilter - class baseCode.dataFilter.RowAbsentFilter.
Filter a data matrix according to flags given in a separate matrix.
RowAbsentFilter() - Constructor for class baseCode.dataFilter.RowAbsentFilter

RowAffyNameFilter - class baseCode.dataFilter.RowAffyNameFilter.
Remove probes that have names meeting certain rules indicating they may have low reliability.
RowAffyNameFilter(int[]) - Constructor for class baseCode.dataFilter.RowAffyNameFilter

RowLevelFilter - class baseCode.dataFilter.RowLevelFilter.
Remove rows from a matrix based on some row-based statistic.
RowLevelFilter() - Constructor for class baseCode.dataFilter.RowLevelFilter

RowMissingFilter - class baseCode.dataFilter.RowMissingFilter.
Remove rows from a matrix that are missing too many points.
RowMissingFilter() - Constructor for class baseCode.dataFilter.RowMissingFilter

RowNameFilter - class baseCode.dataFilter.RowNameFilter.
Remove or retain rows that are on a list.
RowNameFilter(Set, boolean) - Constructor for class baseCode.dataFilter.RowNameFilter

RowNameFilter(Set) - Constructor for class baseCode.dataFilter.RowNameFilter

RowNameFilter() - Constructor for class baseCode.dataFilter.RowNameFilter

range(DoubleArrayList) - Static method in class baseCode.math.Stats
Compute the range of an array.
rankInterpolated(DoubleArrayList, double) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the linearly interpolated number of elements in a list less or equal to a given element.
rankTransform(DoubleArrayList) - Static method in class baseCode.math.Rank
Rank transform an array.
rankTransform(Map) - Static method in class baseCode.math.Rank
Rank transform a map, where the values are numerical (java.lang.Double) values we wish to rank.
rbfNormalize(AbstractNamedDoubleMatrix, double) - Static method in class baseCode.math.MatrixStats
Normalize a matrix in place to be a transition matrix.
read(String) - Method in class baseCode.io.reader.AbstractNamedMatrixReader

read(InputStream) - Method in class baseCode.io.reader.AbstractNamedMatrixReader

read(String) - Method in class baseCode.io.reader.DoubleMatrixReader

read(InputStream) - Method in class baseCode.io.reader.DoubleMatrixReader

read(InputStream, Set) - Method in class baseCode.io.reader.DoubleMatrixReader

read(InputStream, Set, boolean) - Method in class baseCode.io.reader.DoubleMatrixReader

read(String, Set) - Method in class baseCode.io.reader.DoubleMatrixReader
Read a matrix from a file, subject to filtering criteria.
read(String) - Method in class baseCode.io.reader.MapReader

read(InputStream) - Method in class baseCode.io.reader.MapReader

read(String, boolean) - Method in class baseCode.io.reader.MapReader

read(InputStream, boolean) - Method in class baseCode.io.reader.MapReader

read(String) - Method in class baseCode.io.reader.SparseDoubleMatrixReader

read(InputStream) - Method in class baseCode.io.reader.SparseDoubleMatrixReader

read(String, Set) - Method in class baseCode.io.reader.SparseDoubleMatrixReader
Read a matrix from a file, subject to filtering criteria.
read(InputStream, Set) - Method in class baseCode.io.reader.SparseDoubleMatrixReader
Read a sparse matrix that is expressed as an adjacency list in a tab-delimited file:
read(String) - Method in class baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader

read(InputStream) - Method in class baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader
Read an entire sparse matrix from a stream (JW format).
read(InputStream, int) - Method in class baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader
Read an entire sparse matrix from a stream (JW format).
read(String) - Method in class baseCode.io.reader.StringMatrixReader

read(InputStream) - Method in class baseCode.io.reader.StringMatrixReader
Missing values are entered as an empty string.
read(String, DenseDoubleMatrix2DNamed) - Method in class baseCode.misc.GroupMap
The input file format is that used by MapReader.
readFromAdjList(String) - Method in class baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader
Read a sparse symmetric square matrix that is expressed as an adjacency list in a tab-delimited file:
readFromAdjList(InputStream) - Method in class baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader

readHeader(BufferedReader) - Method in class baseCode.io.reader.AbstractNamedMatrixReader

readJW(InputStream) - Method in class baseCode.io.reader.SparseDoubleMatrixReader
Read a sparse matrix in "JW" (Jason Weston) format.
readOneRow(BufferedReader) - Method in class baseCode.io.reader.AbstractNamedMatrixReader

readOneRow(BufferedReader) - Method in class baseCode.io.reader.DoubleMatrixReader

readOneRow(BufferedReader) - Method in class baseCode.io.reader.SparseDoubleMatrixReader

readOneRow(BufferedReader) - Method in class baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader

readOneRow(BufferedReader, int) - Method in class baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader
Use this to read one row from a matrix (JW format).
readOneRow(BufferedReader) - Method in class baseCode.io.reader.StringMatrixReader

readTestResult(InputStream) - Static method in class baseCode.util.RegressionTesting

readTestResult(String) - Static method in class baseCode.util.RegressionTesting

readTestResultFromFile(String) - Static method in class baseCode.util.RegressionTesting

removeAspect(GeneAnnotations, GONames, StatusViewer, String) - Static method in class baseCode.bio.geneset.GeneSetMapTools

removeBySize(GeneAnnotations, StatusViewer, int, int) - Static method in class baseCode.bio.geneset.GeneSetMapTools
Remove gene sets that don't meet certain criteria.
removeClassFromMaps(String) - Method in class baseCode.bio.geneset.GeneAnnotations
Remove a gene set (class) from all the maps that reference it.
repaint(long, int, int, int, int) - Method in class baseCode.gui.table.JBarGraphCellRenderer

repaint(Rectangle) - Method in class baseCode.gui.table.JBarGraphCellRenderer

resetRowKeys() - Method in class baseCode.gui.ColorMatrix

resetRowKeys() - Method in class baseCode.gui.JMatrixDisplay

resetSelectedProbes() - Method in class baseCode.bio.geneset.GeneAnnotations
Set the selected gene set to be the entire set.
resetSelectedSets() - Method in class baseCode.bio.geneset.GeneAnnotations
Set the selected gene set to be the entire set.
revalidate() - Method in class baseCode.gui.table.JBarGraphCellRenderer

revalidate() - Method in class baseCode.gui.table.JMatrixCellRenderer

revalidate() - Method in class baseCode.gui.table.JVerticalHeaderRenderer

rocpval(int, double) - Static method in class baseCode.math.ROC
For an AROC value, calculates a p value based on approximation for calculating the stanadard deviation.
rows() - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix

rows() - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

rows() - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed

rows() - Method in interface baseCode.dataStructure.matrix.NamedMatrix
Get the number of rows the matrix has
rows() - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed

rows() - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed

rows() - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed

run() - Method in class baseCode.algorithm.learning.unsupervised.cluster.HierarchicalClusterer
Perform a hierarchical clustering on the objects.
run(DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
Following CH section 2.2.
run(DoubleArrayList, DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis

run(DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis

runQuery(String) - Method in class baseCode.db.Handle

runUpdateQuery(String) - Method in class baseCode.db.Handle

S

SMALL - Static variable in class baseCode.math.Constants

ST - Static variable in class baseCode.dataFilter.AffymetrixProbeNameFilter
Filter probes that contain the '_st' (sense strand) tag
ST - Static variable in class baseCode.dataFilter.RowAffyNameFilter
Filter probes that contain the '_st' (sense strand) tag
Similarity - interface baseCode.algorithm.learning.unsupervised.cluster.Similarity.

SparseDoubleMatrix2DNamed - class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed.
Title: SparseDoubleMatrix2DNamed
SparseDoubleMatrix2DNamed(double[][]) - Constructor for class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed

SparseDoubleMatrix2DNamed(int, int) - Constructor for class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed

SparseDoubleMatrixReader - class baseCode.io.reader.SparseDoubleMatrixReader.

SparseDoubleMatrixReader() - Constructor for class baseCode.io.reader.SparseDoubleMatrixReader

SparseRaggedDouble2DNamedMatrixReader - class baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader.
Best data structure for reading really big, really sparse matrices when a matrix represetation is needed.
SparseRaggedDouble2DNamedMatrixReader() - Constructor for class baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader

SparseRaggedDoubleMatrix2DNamed - class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed.
A sparse matrix class where the rows are ragged and compressed.
SparseRaggedDoubleMatrix2DNamed() - Constructor for class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed

SpecFunc - class baseCode.math.SpecFunc.
Assorted special functions, primarily concerning probability distributions.
SpecFunc() - Constructor for class baseCode.math.SpecFunc

Stack - class baseCode.dataStructure.Stack.
Deprecated. -- use java.util.List instead.
Stack() - Constructor for class baseCode.dataStructure.Stack
Deprecated. Build a stack with the default capacity.
Stack(int) - Constructor for class baseCode.dataStructure.Stack
Deprecated. Build a stack with a given capacity.
Stats - class baseCode.math.Stats.
Miscellaneous functions used for statistical analysis.
StatusDebugLogger - class baseCode.util.StatusDebugLogger.
Copyright (c) 2004 Columbia University
StatusDebugLogger() - Constructor for class baseCode.util.StatusDebugLogger

StatusJlabel - class baseCode.gui.StatusJlabel.
Title:
StatusJlabel(JLabel) - Constructor for class baseCode.gui.StatusJlabel

StatusStderr - class baseCode.util.StatusStderr.
Prints status info to stderr
StatusStderr() - Constructor for class baseCode.util.StatusStderr

StatusViewer - interface baseCode.util.StatusViewer.
Intended use is to display 'status' information or other messages to users in a non-disruptive fashion (though the actual use is up to the implementer).
StringArrayToBytes(String[]) - Method in class baseCode.io.StringConverter
FIXME this is broken.
StringConverter - class baseCode.io.StringConverter.

StringConverter() - Constructor for class baseCode.io.StringConverter

StringMatrix2DNamed - class baseCode.dataStructure.matrix.StringMatrix2DNamed.
A NamedMatrix containing String objects.
StringMatrix2DNamed(int, int) - Constructor for class baseCode.dataStructure.matrix.StringMatrix2DNamed

StringMatrixReader - class baseCode.io.reader.StringMatrixReader.
Reader for StringMatrix2DNamed
StringMatrixReader() - Constructor for class baseCode.io.reader.StringMatrixReader

StringToDoubles(String) - Method in class baseCode.io.StringConverter

sampleKurtosis(DoubleArrayList, double, double) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the sample kurtosis (aka excess) of a data sequence.
sampleSkew(DoubleArrayList, double, double) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the sample skew of a data sequence.
sampleStandardDeviation(int, double) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the sample standard deviation.
sampleStandardDeviations(DenseDoubleMatrix2DNamed) - Static method in class baseCode.math.MatrixRowStats
Calculates the sample standard deviation of each row of a matrix
sampleVariance(DoubleArrayList, double) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the sample variance of a data sequence.
samplingVariance(double, double) - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
Equation 18-10 from CH.
samplingVariance(double, double, double) - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis
CH eqn 18-7
samplingVariances(DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
Run equation CH 18-10 on a list of sample sizes and effects.
samplingVariances(DoubleArrayList, DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis
Run eqn 18-7 on a set of effect sizes.
saveImage(String) - Method in class baseCode.gui.JMatrixDisplay
Saves the image to a png file.
saveImage(String, boolean) - Method in class baseCode.gui.JMatrixDisplay

saveImage(String, boolean, boolean) - Method in class baseCode.gui.JMatrixDisplay

selectProbes(String) - Method in class baseCode.bio.geneset.GeneAnnotations
Create a selected probes list based on a search string.
selectSets(String, GONames) - Method in class baseCode.bio.geneset.GeneAnnotations

selectedProbes() - Method in class baseCode.bio.geneset.GeneAnnotations

selectedSets() - Method in class baseCode.bio.geneset.GeneAnnotations

set(int, int) - Method in class baseCode.dataStructure.Point

set(int, int, Object) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix

set(int, int, double) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix

set(int, int, Object) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

set(int, int, Object) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed

set(int, int, double) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed

set(int, int, Object) - Method in interface baseCode.dataStructure.matrix.NamedMatrix
Set a value in the matrix.
set(int, int, Object) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed

set(int, int, double) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed

set(int, int, Object) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed

set(int, int, double) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed

set(int, int, Object) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed

setActionButtonText(String) - Method in class baseCode.gui.AppDialog

setAlpha(double) - Method in class baseCode.algorithm.learning.unsupervised.RankProp
controls amount of "clustering"
setAspect(String) - Method in class baseCode.bio.GOEntry

setCancelButtonText(String) - Method in class baseCode.gui.AppDialog

setCellSize(Dimension) - Method in class baseCode.gui.JMatrixDisplay

setColor(int, int, Color) - Method in class baseCode.gui.ColorMatrix

setColorMap(Color[]) - Method in class baseCode.gui.ColorMatrix

setColorMap(Color[]) - Method in class baseCode.gui.JGradientBar

setColorMap(Color[]) - Method in class baseCode.gui.JMatrixDisplay

setColumnComparator(Class, Comparator) - Method in class baseCode.gui.table.TableSorter

setColumnNames(List) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

setColumnNames(List) - Method in interface baseCode.dataStructure.matrix.NamedMatrix

setContents(Object) - Method in class baseCode.dataStructure.tree.BinaryTreeNode

setDefinition(String) - Method in class baseCode.dataStructure.OntologyEntry

setDelimiter(String) - Method in class baseCode.io.StringConverter

setDisplayRange(double, double) - Method in class baseCode.gui.ColorMatrix

setDisplayRange(double, double) - Method in class baseCode.gui.JMatrixDisplay

setElement(Object) - Method in class baseCode.dataStructure.tree.TreeNode

setError(String) - Method in class baseCode.gui.StatusJlabel

setError(String) - Method in class baseCode.util.StatusDebugLogger

setError(String) - Method in class baseCode.util.StatusStderr

setError(String) - Method in interface baseCode.util.StatusViewer
Print an error status messge.
setFilterNames(Set, boolean) - Method in class baseCode.dataFilter.RowNameFilter

setFinishDisabled() - Method in class baseCode.gui.Wizard
Disable the "finish" button, indicating the user has some steps to do yet.
setFinishEnabled() - Method in class baseCode.gui.Wizard
Enable the "finish" button, indicating the user can get out of the wizard at this stage.
setFirstChild(TreeNode) - Method in class baseCode.dataStructure.tree.TreeNode

setFixed(boolean) - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis

setFlagMatrix(StringMatrix2DNamed) - Method in class baseCode.dataFilter.RowAbsentFilter

setGraph(Graph) - Method in class baseCode.dataStructure.graph.AbstractGraphNode
Set the graph this belongs to.
setGraph(Graph) - Method in interface baseCode.dataStructure.graph.GraphNode

setHelpButtonText(String) - Method in class baseCode.gui.AppDialog

setHighCut(double) - Method in class baseCode.dataFilter.AbstractLevelFilter
Set the high threshold for removal.
setHighCut(double, boolean) - Method in class baseCode.dataFilter.AbstractLevelFilter

setItem(Object) - Method in class baseCode.dataStructure.graph.AbstractGraphNode

setItem(Object) - Method in interface baseCode.dataStructure.graph.GraphNode
Set the contents of the node.
setKeepMarginal(boolean) - Method in class baseCode.dataFilter.RowAbsentFilter

setLabels(double, double) - Method in class baseCode.gui.JGradientBar

setLabelsVisible(boolean) - Method in class baseCode.gui.JMatrixDisplay
If this display component has already been added to the GUI, it will be resized to fit or exclude the row names
setLeft(BinaryTreeNode) - Method in class baseCode.dataStructure.tree.BinaryTreeNode

setLowCut(double) - Method in class baseCode.dataFilter.AbstractLevelFilter
Set the low threshold for removal.
setLowCut(double, boolean) - Method in class baseCode.dataFilter.AbstractLevelFilter

setMatrix(ColorMatrix) - Method in class baseCode.gui.JMatrixDisplay

setMaxFractionRemoved(double) - Method in class baseCode.dataFilter.RowMissingFilter
Set the maximum fraction of rows which will be removed from the data set.
setMaxIter(int) - Method in class baseCode.algorithm.learning.unsupervised.RankProp
Maximum iterations before stopping.
setMethod(int) - Method in class baseCode.dataFilter.RowLevelFilter
Choose the method that will be used for filtering.
setMinPresentCount(int) - Method in class baseCode.dataFilter.RowAbsentFilter

setMinPresentCount(int) - Method in class baseCode.dataFilter.RowMissingFilter
Set the minimum number of values that must be present in each row.
setMinPresentFraction(double) - Method in class baseCode.dataFilter.RowAbsentFilter

setMinPresentFraction(double) - Method in class baseCode.dataFilter.RowMissingFilter

setName(String) - Method in class baseCode.dataStructure.OntologyEntry

setNextSibling(TreeNode) - Method in class baseCode.dataStructure.tree.TreeNode

setQuick(int, int, double) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed

setQuick(int, double) - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D

setQuick(int, int, double) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed

setQuick(int, int, Object) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed

setRemoveAllNegative(boolean) - Method in class baseCode.dataFilter.RowLevelFilter
Set the filter to remove all rows that have only negative values.
setRight(BinaryTreeNode) - Method in class baseCode.dataStructure.tree.BinaryTreeNode

setRoot(BinaryTreeNode) - Method in class baseCode.dataStructure.tree.BinaryTree

setRow(int, double[]) - Method in class baseCode.gui.ColorMatrix
Changes values in a row, clipping if there are more values than columns.
setRowHeight(int) - Method in class baseCode.gui.JMatrixDisplay

setRowKeys(int[]) - Method in class baseCode.gui.ColorMatrix

setRowKeys(int[]) - Method in class baseCode.gui.JMatrixDisplay

setRowNames(List) - Method in class baseCode.dataStructure.matrix.AbstractNamedMatrix

setRowNames(List) - Method in interface baseCode.dataStructure.matrix.NamedMatrix

setSortingStatus(int, int) - Method in class baseCode.gui.table.TableSorter

setStandardizedEnabled(boolean) - Method in class baseCode.gui.JMatrixDisplay

setStatus(String) - Method in class baseCode.gui.StatusJlabel

setStatus(String) - Method in class baseCode.util.StatusDebugLogger

setStatus(String) - Method in class baseCode.util.StatusStderr

setStatus(String) - Method in interface baseCode.util.StatusViewer
Print the status to the location appropriate for this application.
setTableHeader(JTableHeader) - Method in class baseCode.gui.table.TableSorter

setTableModel(TableModel) - Method in class baseCode.gui.table.TableSorter

setText(String) - Method in class baseCode.gui.JLinkLabel

setText(String, String) - Method in class baseCode.gui.JLinkLabel

setTopoSortOrder(int) - Method in class baseCode.dataStructure.graph.DirectedGraphNode

setTransform(boolean) - Method in class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis

setURL(String) - Method in class baseCode.gui.JLinkLabel

setUseAsFraction(boolean) - Method in class baseCode.dataFilter.AbstractLevelFilter
Set the filter to interpret the low and high cuts as fractions; that is, if true, lowcut 0.1 means remove 0.1 of the rows with the lowest values.
setUseHighCutAsFraction(boolean) - Method in class baseCode.dataFilter.AbstractLevelFilter

setUseLowCutAsFraction(boolean) - Method in class baseCode.dataFilter.AbstractLevelFilter

setValue(Object, Object) - Method in class baseCode.dataStructure.graph.AbstractGraphNode

setValue(Object, Object) - Method in interface baseCode.dataStructure.graph.GraphNode
Set the key and value associated with this node.
setValueAt(Object, int, int) - Method in class baseCode.gui.table.TableSorter

showDialog() - Method in class baseCode.gui.AppDialog

showError(String) - Method in class baseCode.gui.Wizard
Print an error message to the status bar.
showError(String) - Method in class baseCode.gui.WizardStep
Print an error message to the status bar.
showStatus(String) - Method in class baseCode.gui.Wizard
Print a message to the status bar.
showStatus(String) - Method in class baseCode.gui.WizardStep
Print a message to the status bar.
showWizard() - Method in class baseCode.gui.Wizard

similarity() - Method in interface baseCode.algorithm.learning.unsupervised.cluster.Similarity

size() - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed

size() - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed

size() - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed

sizeWithoutMissingValues(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
Return the size of the list, ignoring missing values.
skew(DoubleArrayList, double, double) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the skew of a data sequence, which is moment(data,3,mean) / standardDeviation³.
sortGeneSets() - Method in class baseCode.bio.geneset.GeneAnnotations
Sort the gene sets, filling out the sortedGeneSets.
sortGeneSetsBySize() - Method in class baseCode.bio.geneset.GeneAnnotations

sparse(double[][]) - Static method in class baseCode.dataStructure.matrix.DoubleMatrix2DNamedFactory

sparse(int, int) - Static method in class baseCode.dataStructure.matrix.DoubleMatrix2DNamedFactory

spearmanRankCorrelation(DoubleArrayList, DoubleArrayList) - Static method in class baseCode.math.Distance
Spearman Rank Correlation.
standardize() - Method in class baseCode.gui.ColorMatrix
Normalizes the elements of a matrix to variance one and mean zero, ignoring missing values todo move this to matrixstats or something.
standardize(DoubleArrayList, double, double) - Static method in class baseCode.math.DescriptiveWithMissing
Modifies a data sequence to be standardized.
standardize(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
Standardize.
stringPixelWidth(String, Font, Component) - Static method in class baseCode.graphics.text.Util

sum(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the sum of a data sequence.
sumOfInversions(DoubleArrayList, int, int) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the sum of inversions of a data sequence, which is Sum( 1.0 / data[i]).
sumOfLogarithms(DoubleArrayList, int, int) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the sum of logarithms of a data sequence, which is Sum( Log(data[i]).
sumOfPowerDeviations(DoubleArrayList, int, double) - Static method in class baseCode.math.DescriptiveWithMissing
Returns Sum( (data[i]-c)^k ); optimized for common parameters like c == 0.0 and/or k == -2 ..
sumOfPowerDeviations(DoubleArrayList, int, double, int, int) - Static method in class baseCode.math.DescriptiveWithMissing
Returns Sum( (data[i]-c)^k ) for all i = from ..
sumOfPowers(DoubleArrayList, int) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the sum of powers of a data sequence, which is Sum ( data[i]^k ).
sumOfSquaredDeviations(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
Compute the sum of the squared deviations from the mean of a data sequence.
sumOfSquares(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing
Returns the sum of squares of a data sequence.
sumOfSquares(DenseDoubleMatrix2DNamed) - Static method in class baseCode.math.MatrixRowStats
Calculates the sum of squares for each row of a matrix
sums(DenseDoubleMatrix2DNamed) - Static method in class baseCode.math.MatrixRowStats
Calculate the sums of a matrix's rows.
T TINY - Static variable in class baseCode.math.Constants TXT_EXTENSION - Static variable in class baseCode.util.FileTools TableSorter - class baseCode.gui.table.TableSorter. TableSorter is a decorator for TableModels; adding sorting functionality to a supplied TableModel. TableSorter() - Constructor for class baseCode.gui.table.TableSorter TableSorter(TableModel) - Constructor for class baseCode.gui.table.TableSorter TableSorter(TableModel, JTableHeader) - Constructor for class baseCode.gui.table.TableSorter TableSorter(TableModel, JMatrixDisplay) - Constructor for class baseCode.gui.table.TableSorter Tree - class baseCode.dataStructure.tree.Tree. Tree() - Constructor for class baseCode.dataStructure.tree.Tree TreeNode - class baseCode.dataStructure.tree.TreeNode. TreeNode(Object) - Constructor for class baseCode.dataStructure.tree.TreeNode TreePanel - class baseCode.gui.TreePanel. Copyright (c) Columbia University TreePanel(JTree) - Constructor for class baseCode.gui.TreePanel tableModel - Variable in class baseCode.gui.table.TableSorter testDir(String) - Static method in class baseCode.gui.GuiUtil testDir(String) - Static method in class baseCode.util.FileTools testFile(String) - Static method in class baseCode.gui.GuiUtil testFile(String) - Static method in class baseCode.util.FileTools testFile(File) - Static method in class baseCode.util.FileTools toArray() - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix1D WARNING unlike the superclass, this returns the actual underlying array, not a copy. toArray() - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed toCollection() - Method in class baseCode.algorithm.learning.unsupervised.cluster.Cluster toCollection() - Method in class baseCode.common.Distanceable Return a collections view of the object. toString() - Method in class baseCode.dataStructure.Link toString() - Method in class baseCode.dataStructure.OntologyEntry toString() - Method in class baseCode.dataStructure.Point toString() - Method in class baseCode.dataStructure.graph.AbstractGraphNode toString() - Method in class baseCode.dataStructure.graph.DirectedGraph Shows the tree as a tabbed list. toString() - Method in class baseCode.dataStructure.graph.DirectedGraphNode toString() - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed toString() - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D toString() - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed toString() - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed toString() - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed toString() - Method in class baseCode.gui.JLinkLabel toTableModel() - Method in class baseCode.bio.geneset.GeneAnnotations top() - Method in class baseCode.dataStructure.Stack Deprecated. Get the most recently added item, without removing it. topoSort() - Method in class baseCode.dataStructure.graph.DirectedGraph Fills in the topoSortOrder for each node. topoSortOrder - Variable in class baseCode.dataStructure.graph.DirectedGraphNode treeView() - Method in class baseCode.dataStructure.graph.DirectedGraph Generate a JTree corresponding to this graph. trimToSize() - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed trimmedMean(DoubleArrayList, double, int, int) - Static method in class baseCode.math.DescriptiveWithMissing Returns the trimmed mean of a sorted data sequence. twoSample(DoubleArrayList, DoubleArrayList) - Static method in class baseCode.math.KSTest U UndirectedGraphNode - class baseCode.dataStructure.graph.UndirectedGraphNode. Copyright (c) Columbia University UndirectedGraphNode(Object, Object, AbstractGraph) - Constructor for class baseCode.dataStructure.graph.UndirectedGraphNode UndirectedGraphNode(Object) - Constructor for class baseCode.dataStructure.graph.UndirectedGraphNode UniformDensityComputer - class baseCode.math.distribution.UniformDensityComputer. UniformDensityComputer() - Constructor for class baseCode.math.distribution.UniformDensityComputer Create a UniformDensityComputer where the density is defined over the unit inteval [0,1]. UniformDensityComputer(double, double) - Constructor for class baseCode.math.distribution.UniformDensityComputer Create a UniformDensityComputer where the density is defined over the interval given UniformProbabilityComputer - class baseCode.math.distribution.UniformProbabilityComputer. Generate probabilities from the uniform distribution. UniformProbabilityComputer() - Constructor for class baseCode.math.distribution.UniformProbabilityComputer Create a UniformProbabilityComputer where the density is defined over the unit inteval [0,1]. UniformProbabilityComputer(double, double) - Constructor for class baseCode.math.distribution.UniformProbabilityComputer Create a UniformProbabilityComputer where the density is defined over the interval given Util - class baseCode.graphics.text.Util. Util() - Constructor for class baseCode.graphics.text.Util unFisherTransform(double) - Static method in class baseCode.math.CorrelationStats Reverse the Fisher z-transform of correlations. unMark() - Method in class baseCode.common.Visitable unMark() - Method in class baseCode.dataStructure.graph.AbstractGraphNode unmarkAll() - Method in class baseCode.dataStructure.graph.AbstractGraph Reset the 'visited' marks of the graph to false. unmarkAll() - Method in interface baseCode.dataStructure.graph.Graph useHighAsFraction - Variable in class baseCode.dataFilter.AbstractLevelFilter useLowAsFraction - Variable in class baseCode.dataFilter.AbstractLevelFilter V Visitable - class baseCode.common.Visitable. Visitable() - Constructor for class baseCode.common.Visitable validate() - Method in class baseCode.gui.table.JBarGraphCellRenderer validate() - Method in class baseCode.gui.table.JMatrixCellRenderer validate() - Method in class baseCode.gui.table.JVerticalHeaderRenderer valueChanged(TreeSelectionEvent) - Method in class baseCode.gui.TreePanel values - Variable in class baseCode.dataStructure.matrix.RCDoubleMatrix1D variance(DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing Provided for convenience! viewColumn(int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed viewColumn(int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed viewColumn(int) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed viewRow(int) - Method in class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix viewRow(int) - Method in class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed viewRow(int) - Method in class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed viewRow(int) - Method in class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed viewRow(int) - Method in class baseCode.dataStructure.matrix.StringMatrix2DNamed viewSelectionLike(int[]) - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D visited - Variable in class baseCode.dataStructure.graph.AbstractGraphNode W Wishart - class baseCode.math.distribution.Wishart. Wishart distribution, used to simulate covariance matrices. Wishart(double, DoubleMatrix2D, RandomEngine) - Constructor for class baseCode.math.distribution.Wishart Wizard - class baseCode.gui.Wizard. Wizard(JFrame, int, int) - Constructor for class baseCode.gui.Wizard WizardStep - class baseCode.gui.WizardStep. Title: WizardStep(Wizard) - Constructor for class baseCode.gui.WizardStep weightedMean(DoubleArrayList, DoubleArrayList) - Static method in class baseCode.math.DescriptiveWithMissing Returns the weighted mean of a data sequence. weightedMean(DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.metaanalysis.MetaAnalysis General formula for weighted mean of effect sizes. weightedMean(DoubleArrayList, DoubleArrayList, DoubleArrayList) - Method in class baseCode.math.metaanalysis.MetaAnalysis General formula for weighted mean of effect sizes including quality index scores for each value. winsorizedMean(DoubleArrayList, double, int, int) - Static method in class baseCode.math.DescriptiveWithMissing Not supported. worst() - Method in class baseCode.algorithm.Ranker write(IHistogram1D, Writer) - Method in class baseCode.io.writer.HistogramWriter Print out a IHistogram1D object. write(IHistogram1D, OutputStream) - Method in class baseCode.io.writer.HistogramWriter Print to a stream. writeTestResult(String, String) - Static method in class baseCode.util.RegressionTesting X X - Static variable in class baseCode.dataFilter.AffymetrixProbeNameFilter Filter probes that have the "_x_at" tag. X - Static variable in class baseCode.dataFilter.RowAffyNameFilter Filter probes that have the "_x_at" tag. XMLFileFilter - class baseCode.gui.file.XMLFileFilter. XMLFileFilter() - Constructor for class baseCode.gui.file.XMLFileFilter XML_EXTENSIONS - Static variable in class baseCode.util.FileTools Z zDotProduct(DoubleMatrix1D) - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D zSum() - Method in class baseCode.dataStructure.matrix.RCDoubleMatrix1D A B C D E F G H I J K L M N O P Q R S T U V W X Z Overview Package Class Use Tree Deprecated Index Help PREV NEXT FRAMES NO FRAMES Copyright © 2003-2005 Columbia University. All Rights Reserved.